feat(ipuaro): add JSON tool call parsing and improve prompts

- Add JSON fallback parsing in ResponseParser for LLMs that prefer JSON
- Add tool name aliases (get_functions -> get_lines, etc.)
- Improve system prompt with clear tool usage guidelines
- Add native Ollama tools support in OllamaClient
- Add E2E tests for full workflow with real Ollama

packages/guardian/docs/RESEARCH_CITATIONS.md

@@ -20,6 +20,21 @@ This document provides authoritative sources, academic papers, industry standard
 12. [Aggregate Boundary Validation (DDD Tactical Patterns)](#12-aggregate-boundary-validation-ddd-tactical-patterns)
 13. [Secret Detection & Security](#13-secret-detection--security)
 14. [Severity-Based Prioritization & Technical Debt](#14-severity-based-prioritization--technical-debt)
+15. [Domain Event Usage Validation](#15-domain-event-usage-validation)
+16. [Value Object Immutability](#16-value-object-immutability)
+17. [Command Query Separation (CQS/CQRS)](#17-command-query-separation-cqscqrs)
+18. [Factory Pattern](#18-factory-pattern)
+19. [Specification Pattern](#19-specification-pattern)
+20. [Bounded Context](#20-bounded-context)
+21. [Persistence Ignorance](#21-persistence-ignorance)
+22. [Null Object Pattern](#22-null-object-pattern)
+23. [Primitive Obsession](#23-primitive-obsession)
+24. [Service Locator Anti-pattern](#24-service-locator-anti-pattern)
+25. [Double Dispatch and Visitor Pattern](#25-double-dispatch-and-visitor-pattern)
+26. [Entity Identity](#26-entity-identity)
+27. [Saga Pattern](#27-saga-pattern)
+28. [Anti-Corruption Layer](#28-anti-corruption-layer)
+29. [Ubiquitous Language](#29-ubiquitous-language)
 
 ---
 
@@ -801,22 +816,840 @@ This document provides authoritative sources, academic papers, industry standard
 
 ---
 
+## 15. Domain Event Usage Validation
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Original Definition:**
+- Domain Events: "Something happened that domain experts care about"
+- Events capture facts about the domain that have already occurred
+- Distinct from system events - they model business-relevant occurrences
+- Reference: [Martin Fowler - Domain Event](https://martinfowler.com/eaaDev/DomainEvent.html)
+
+**Book: Domain-Driven Design** (2003)
+- Author: Eric Evans
+- Publisher: Addison-Wesley Professional
+- ISBN: 978-0321125217
+- Domain Events weren't explicitly in the original book but evolved from DDD community
+- Reference: [DDD Community - Domain Events](https://www.domainlanguage.com/)
+
+### Vaughn Vernon: Implementing Domain-Driven Design (2013)
+
+**Chapter 8: Domain Events**
+- Author: Vaughn Vernon
+- Comprehensive coverage of Domain Events implementation
+- "Model information about activity in the domain as a series of discrete events"
+- Reference: [Amazon - Implementing DDD](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+**Key Principles:**
+- Events should be immutable
+- Named in past tense (OrderPlaced, UserRegistered)
+- Contain all data needed by handlers
+- Enable loose coupling between aggregates
+
+### Martin Fowler's Event Patterns
+
+**Event Sourcing:**
+- "Capture all changes to an application state as a sequence of events"
+- Events become the primary source of truth
+- Reference: [Martin Fowler - Event Sourcing](https://martinfowler.com/eaaDev/EventSourcing.html)
+
+**Event-Driven Architecture:**
+- Promotes loose coupling between components
+- Enables asynchronous processing
+- Reference: [Martin Fowler - Event-Driven](https://martinfowler.com/articles/201701-event-driven.html)
+
+### Why Direct Infrastructure Calls Are Bad
+
+**Coupling Issues:**
+- Direct calls create tight coupling between domain and infrastructure
+- Makes testing difficult (need to mock infrastructure)
+- Violates Single Responsibility Principle
+- Reference: [Microsoft - Domain Events Design](https://learn.microsoft.com/en-us/dotnet/architecture/microservices/microservice-ddd-cqrs-patterns/domain-events-design-implementation)
+
+**Benefits of Domain Events:**
+- Decouples domain from side effects
+- Enables eventual consistency
+- Improves testability
+- Supports audit logging naturally
+- Reference: [Jimmy Bogard - Domain Events](https://lostechies.com/jimmybogard/2010/04/08/strengthening-your-domain-domain-events/)
+
+---
+
+## 16. Value Object Immutability
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Value Object Definition:**
+- "An object that describes some characteristic or attribute but carries no concept of identity"
+- "Value Objects should be immutable"
+- When you care only about the attributes of an element, classify it as a Value Object
+- Reference: [Martin Fowler - Value Object](https://martinfowler.com/bliki/ValueObject.html)
+
+**Immutability Requirement:**
+- "Treat the Value Object as immutable"
+- "Don't give it any identity and avoid the design complexities necessary to maintain Entities"
+- Reference: [DDD Reference - Value Objects](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+### Martin Fowler on Value Objects
+
+**Blog Post: Value Object** (2016)
+- "A small simple object, like money or a date range, whose equality isn't based on identity"
+- "I consider value objects to be one of the most important building blocks of good domain models"
+- Reference: [Martin Fowler - Value Object](https://martinfowler.com/bliki/ValueObject.html)
+
+**Key Properties:**
+- Equality based on attribute values, not identity
+- Should be immutable (once created, cannot be changed)
+- Side-effect free behavior
+- Self-validating (validate in constructor)
+
+### Vaughn Vernon: Implementing DDD
+
+**Chapter 6: Value Objects**
+- Detailed implementation guidance
+- "Measures, quantifies, or describes a thing in the domain"
+- "Can be compared with other Value Objects using value equality"
+- "Completely replaceable when the measurement changes"
+- Reference: [Vaughn Vernon - Implementing DDD](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+### Why Immutability Matters
+
+**Thread Safety:**
+- Immutable objects are inherently thread-safe
+- No synchronization needed for concurrent access
+- Reference: [Effective Java - Item 17](https://www.amazon.com/Effective-Java-Joshua-Bloch/dp/0134685997)
+
+**Reasoning About Code:**
+- Easier to understand code when objects don't change
+- No defensive copying needed
+- Simplifies caching and optimization
+- Reference: [Oracle Java Tutorials - Immutable Objects](https://docs.oracle.com/javase/tutorial/essential/concurrency/immutable.html)
+
+**Functional Programming Influence:**
+- Immutability is a core principle of functional programming
+- Reduces side effects and makes code more predictable
+- Reference: [Wikipedia - Immutable Object](https://en.wikipedia.org/wiki/Immutable_object)
+
+---
+
+## 17. Command Query Separation (CQS/CQRS)
+
+### Bertrand Meyer: Original CQS Principle
+
+**Book: Object-Oriented Software Construction** (1988, 2nd Ed. 1997)
+- Author: Bertrand Meyer
+- Publisher: Prentice Hall
+- ISBN: 978-0136291558
+- Introduced Command Query Separation principle
+- Reference: [Wikipedia - CQS](https://en.wikipedia.org/wiki/Command%E2%80%93query_separation)
+
+**CQS Principle:**
+- "Every method should either be a command that performs an action, or a query that returns data to the caller, but not both"
+- Commands: change state, return nothing (void)
+- Queries: return data, change nothing (side-effect free)
+- Reference: [Martin Fowler - CommandQuerySeparation](https://martinfowler.com/bliki/CommandQuerySeparation.html)
+
+### Greg Young: CQRS Pattern
+
+**CQRS Documents** (2010)
+- Author: Greg Young
+- Extended CQS to architectural pattern
+- "CQRS is simply the creation of two objects where there was previously only one"
+- Reference: [Greg Young - CQRS Documents](https://cqrs.files.wordpress.com/2010/11/cqrs_documents.pdf)
+
+**Key Concepts:**
+- Separate models for reading and writing
+- Write model (commands) optimized for business logic
+- Read model (queries) optimized for display/reporting
+- Reference: [Microsoft - CQRS Pattern](https://learn.microsoft.com/en-us/azure/architecture/patterns/cqrs)
+
+### Martin Fowler on CQRS
+
+**Blog Post: CQRS** (2011)
+- "At its heart is the notion that you can use a different model to update information than the model you use to read information"
+- Warns against overuse: "CQRS is a significant mental leap for all concerned"
+- Reference: [Martin Fowler - CQRS](https://martinfowler.com/bliki/CQRS.html)
+
+### Benefits and Trade-offs
+
+**Benefits:**
+- Independent scaling of read and write workloads
+- Optimized data schemas for each side
+- Improved security (separate read/write permissions)
+- Reference: [AWS - CQRS Pattern](https://docs.aws.amazon.com/prescriptive-guidance/latest/modernization-data-persistence/cqrs-pattern.html)
+
+**Trade-offs:**
+- Increased complexity
+- Eventual consistency challenges
+- More code to maintain
+- Reference: [Microsoft - CQRS Considerations](https://learn.microsoft.com/en-us/azure/architecture/patterns/cqrs#issues-and-considerations)
+
+---
+
+## 18. Factory Pattern
+
+### Gang of Four: Design Patterns (1994)
+
+**Book: Design Patterns: Elements of Reusable Object-Oriented Software**
+- Authors: Erich Gamma, Richard Helm, Ralph Johnson, John Vlissides (Gang of Four)
+- Publisher: Addison-Wesley
+- ISBN: 978-0201633610
+- Defines Factory Method and Abstract Factory patterns
+- Reference: [Wikipedia - Design Patterns](https://en.wikipedia.org/wiki/Design_Patterns)
+
+**Factory Method Pattern:**
+- "Define an interface for creating an object, but let subclasses decide which class to instantiate"
+- Lets a class defer instantiation to subclasses
+- Reference: [Refactoring Guru - Factory Method](https://refactoring.guru/design-patterns/factory-method)
+
+**Abstract Factory Pattern:**
+- "Provide an interface for creating families of related or dependent objects without specifying their concrete classes"
+- Reference: [Refactoring Guru - Abstract Factory](https://refactoring.guru/design-patterns/abstract-factory)
+
+### Eric Evans: Factory in DDD Context
+
+**Domain-Driven Design** (2003)
+- Chapter 6: "The Life Cycle of a Domain Object"
+- Factories encapsulate complex object creation
+- "Shift the responsibility for creating instances of complex objects and Aggregates to a separate object"
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+**DDD Factory Guidelines:**
+- Factory should create valid objects (invariants satisfied)
+- Two types: Factory for new objects, Factory for reconstitution
+- Keep creation logic out of the entity itself
+- Reference: Already in Section 10 - Domain-Driven Design
+
+### Why Factories Matter in DDD
+
+**Encapsulation of Creation Logic:**
+- Complex aggregates need coordinated creation
+- Business rules should be enforced at creation time
+- Clients shouldn't know construction details
+- Reference: [Vaughn Vernon - Implementing DDD, Chapter 11](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+**Factory vs Constructor:**
+- Constructors should be simple (assign values)
+- Factories handle complex creation logic
+- Factories can return different types
+- Reference: [Effective Java - Item 1: Static Factory Methods](https://www.amazon.com/Effective-Java-Joshua-Bloch/dp/0134685997)
+
+---
+
+## 19. Specification Pattern
+
+### Eric Evans & Martin Fowler
+
+**Original Paper: Specifications** (1997)
+- Authors: Eric Evans and Martin Fowler
+- Introduced the Specification pattern
+- "A Specification states a constraint on the state of another object"
+- Reference: [Martin Fowler - Specification](https://martinfowler.com/apsupp/spec.pdf)
+
+**Domain-Driven Design** (2003)
+- Chapter 9: "Making Implicit Concepts Explicit"
+- Specifications make business rules explicit and reusable
+- "Create explicit predicate-like Value Objects for specialized purposes"
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+### Pattern Definition
+
+**Core Concept:**
+- Specification is a predicate that determines if an object satisfies some criteria
+- Encapsulates business rules that can be reused and combined
+- Reference: [Wikipedia - Specification Pattern](https://en.wikipedia.org/wiki/Specification_pattern)
+
+**Three Main Uses:**
+1. **Selection**: Finding objects that match criteria
+2. **Validation**: Checking if object satisfies rules
+3. **Construction**: Describing what needs to be created
+- Reference: [Martin Fowler - Specification](https://martinfowler.com/apsupp/spec.pdf)
+
+### Composite Specifications
+
+**Combining Specifications:**
+- AND: Both specifications must be satisfied
+- OR: Either specification must be satisfied
+- NOT: Specification must not be satisfied
+- Reference: [Refactoring Guru - Specification Pattern](https://refactoring.guru/design-patterns/specification)
+
+**Benefits:**
+- Reusable business rules
+- Testable in isolation
+- Readable domain language
+- Composable for complex rules
+- Reference: [Enterprise Craftsmanship - Specification Pattern](https://enterprisecraftsmanship.com/posts/specification-pattern-c-implementation/)
+
+---
+
+## 20. Bounded Context
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Original Definition:**
+- "A Bounded Context delimits the applicability of a particular model"
+- "Explicitly define the context within which a model applies"
+- Chapter 14: "Maintaining Model Integrity"
+- Reference: [Martin Fowler - Bounded Context](https://martinfowler.com/bliki/BoundedContext.html)
+
+**Key Principles:**
+- Each Bounded Context has its own Ubiquitous Language
+- Same term can mean different things in different contexts
+- Models should not be shared across context boundaries
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+### Vaughn Vernon: Strategic Design
+
+**Implementing Domain-Driven Design** (2013)
+- Chapter 2: "Domains, Subdomains, and Bounded Contexts"
+- Detailed guidance on identifying and mapping contexts
+- Reference: [Vaughn Vernon - Implementing DDD](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+**Context Mapping Patterns:**
+- Shared Kernel
+- Customer/Supplier
+- Conformist
+- Anti-Corruption Layer
+- Open Host Service / Published Language
+- Reference: [Context Mapping Patterns](https://www.infoq.com/articles/ddd-contextmapping/)
+
+### Why Bounded Contexts Matter
+
+**Avoiding Big Ball of Mud:**
+- Without explicit boundaries, models become entangled
+- Different teams step on each other's models
+- Reference: [Wikipedia - Big Ball of Mud](https://en.wikipedia.org/wiki/Big_ball_of_mud)
+
+**Microservices and Bounded Contexts:**
+- "Microservices should be designed around business capabilities, aligned with bounded contexts"
+- Each microservice typically represents one bounded context
+- Reference: [Microsoft - Microservices and Bounded Contexts](https://learn.microsoft.com/en-us/azure/architecture/microservices/model/domain-analysis)
+
+### Cross-Context Communication
+
+**Integration Patterns:**
+- Never share domain models across contexts
+- Use integration events or APIs
+- Translate between context languages
+- Reference: [Microsoft - Tactical DDD](https://learn.microsoft.com/en-us/azure/architecture/microservices/model/tactical-ddd)
+
+---
+
+## 21. Persistence Ignorance
+
+### Definition and Principles
+
+**Core Concept:**
+- Domain objects should have no knowledge of how they are persisted
+- Business logic remains pure and testable
+- Infrastructure concerns are separated from domain
+- Reference: [Microsoft - Persistence Ignorance](https://learn.microsoft.com/en-us/dotnet/architecture/microservices/microservice-ddd-cqrs-patterns/infrastructure-persistence-layer-design#the-persistence-ignorance-principle)
+
+**Wikipedia Definition:**
+- "Persistence ignorance is the ability of a class to be used without any underlying persistence mechanism"
+- Objects don't know if/how they'll be stored
+- Reference: [Wikipedia - Persistence Ignorance](https://en.wikipedia.org/wiki/Persistence_ignorance)
+
+### Eric Evans: DDD and Persistence
+
+**Domain-Driven Design** (2003)
+- Repositories abstract away persistence details
+- Domain model should not reference ORM or database concepts
+- Reference: Already covered in Section 6 - Repository Pattern
+
+**Key Quote:**
+- "The domain layer should be kept clean of all technical concerns"
+- ORM annotations violate this principle
+- Reference: [Clean Architecture and DDD](https://herbertograca.com/2017/11/16/explicit-architecture-01-ddd-hexagonal-onion-clean-cqrs-how-i-put-it-all-together/)
+
+### Clean Architecture Alignment
+
+**Robert C. Martin:**
+- "The database is a detail"
+- Domain entities should not depend on persistence frameworks
+- Use Repository interfaces to abstract persistence
+- Reference: [Clean Architecture Book](https://www.amazon.com/Clean-Architecture-Craftsmans-Software-Structure/dp/0134494164)
+
+### Practical Implementation
+
+**Two-Model Approach:**
+- Domain Model: Pure business objects
+- Persistence Model: ORM-annotated entities
+- Mappers translate between them
+- Reference: [Microsoft - Infrastructure Layer](https://learn.microsoft.com/en-us/dotnet/architecture/microservices/microservice-ddd-cqrs-patterns/infrastructure-persistence-layer-design)
+
+**Benefits:**
+- Domain model can evolve independently of database schema
+- Easier testing (no ORM required)
+- Database can be changed without affecting domain
+- Reference: [Enterprise Craftsmanship - Persistence Ignorance](https://enterprisecraftsmanship.com/posts/persistence-ignorance/)
+
+---
+
+## 22. Null Object Pattern
+
+### Original Pattern
+
+**Pattern Languages of Program Design 3** (1997)
+- Author: Bobby Woolf
+- Chapter: "Null Object"
+- Publisher: Addison-Wesley
+- ISBN: 978-0201310115
+- Reference: [Wikipedia - Null Object Pattern](https://en.wikipedia.org/wiki/Null_object_pattern)
+
+**Definition:**
+- "A Null Object provides a 'do nothing' behavior, hiding the details from its collaborators"
+- Replaces null checks with polymorphism
+- Reference: [Refactoring Guru - Null Object](https://refactoring.guru/introduce-null-object)
+
+### Martin Fowler's Coverage
+
+**Refactoring Book** (1999, 2018)
+- "Introduce Null Object" refactoring
+- "Replace conditional logic that checks for null with a null object"
+- Reference: [Refactoring Catalog](https://refactoring.com/catalog/introduceNullObject.html)
+
+**Special Case Pattern:**
+- More general pattern that includes Null Object
+- "A subclass that provides special behavior for particular cases"
+- Reference: [Martin Fowler - Special Case](https://martinfowler.com/eaaCatalog/specialCase.html)
+
+### Benefits
+
+**Eliminates Null Checks:**
+- Reduces cyclomatic complexity
+- Cleaner, more readable code
+- Follows "Tell, Don't Ask" principle
+- Reference: [SourceMaking - Null Object](https://sourcemaking.com/design_patterns/null_object)
+
+**Polymorphism Over Conditionals:**
+- Null Object responds to same interface as real object
+- Default/neutral behavior instead of null checks
+- Reference: [C2 Wiki - Null Object](https://wiki.c2.com/?NullObject)
+
+### When to Use
+
+**Good Candidates:**
+- Objects frequently checked for null
+- Null represents "absence" with sensible default behavior
+- Reference: [Baeldung - Null Object Pattern](https://www.baeldung.com/java-null-object-pattern)
+
+**Cautions:**
+- Don't use when null has semantic meaning
+- Can hide bugs if misapplied
+- Reference: [Stack Overflow - Null Object Considerations](https://stackoverflow.com/questions/1274792/is-the-null-object-pattern-a-bad-practice)
+
+---
+
+## 23. Primitive Obsession
+
+### Code Smell Definition
+
+**Martin Fowler: Refactoring** (1999, 2018)
+- Primitive Obsession is a code smell
+- "Using primitives instead of small objects for simple tasks"
+- Reference: [Refactoring Catalog](https://refactoring.com/catalog/)
+
+**Wikipedia Definition:**
+- "Using primitive data types to represent domain ideas"
+- Example: Using string for email, int for money
+- Reference: [Wikipedia - Code Smell](https://en.wikipedia.org/wiki/Code_smell)
+
+### Why It's a Problem
+
+**Lost Type Safety:**
+- String can contain anything, Email cannot
+- Compiler can't catch domain errors
+- Reference: [Refactoring Guru - Primitive Obsession](https://refactoring.guru/smells/primitive-obsession)
+
+**Scattered Validation:**
+- Same validation repeated in multiple places
+- Violates DRY principle
+- Reference: [SourceMaking - Primitive Obsession](https://sourcemaking.com/refactoring/smells/primitive-obsession)
+
+**Missing Behavior:**
+- Primitives can't have domain-specific methods
+- Logic lives in services instead of objects
+- Reference: [Enterprise Craftsmanship - Primitive Obsession](https://enterprisecraftsmanship.com/posts/functional-c-primitive-obsession/)
+
+### Solutions
+
+**Replace with Value Objects:**
+- Money instead of decimal
+- Email instead of string
+- PhoneNumber instead of string
+- Reference: Already covered in Section 16 - Value Object Immutability
+
+**Replace Data Value with Object:**
+- Refactoring: "Replace Data Value with Object"
+- Introduce Parameter Object for related primitives
+- Reference: [Refactoring - Replace Data Value with Object](https://refactoring.com/catalog/replaceDataValueWithObject.html)
+
+### Common Primitive Obsession Examples
+
+**Frequently Misused Primitives:**
+- string for: email, phone, URL, currency code, country code
+- int/decimal for: money, percentage, age, quantity
+- DateTime for: date ranges, business dates
+- Reference: [DDD - Value Objects](https://martinfowler.com/bliki/ValueObject.html)
+
+---
+
+## 24. Service Locator Anti-pattern
+
+### Martin Fowler's Analysis
+
+**Blog Post: Inversion of Control Containers and the Dependency Injection pattern** (2004)
+- Compares Service Locator with Dependency Injection
+- "With service locator the application class asks for it explicitly by a message to the locator"
+- Reference: [Martin Fowler - Inversion of Control](https://martinfowler.com/articles/injection.html)
+
+**Service Locator Definition:**
+- "The basic idea behind a service locator is to have an object that knows how to get hold of all of the services that an application might need"
+- Acts as a registry that provides dependencies on demand
+- Reference: [Martin Fowler - Service Locator](https://martinfowler.com/articles/injection.html#UsingAServiceLocator)
+
+### Why It's Considered an Anti-pattern
+
+**Mark Seemann: Dependency Injection in .NET** (2011, 2nd Ed. 2019)
+- Author: Mark Seemann
+- Extensively covers why Service Locator is problematic
+- "Service Locator is an anti-pattern"
+- Reference: [Mark Seemann - Service Locator is an Anti-Pattern](https://blog.ploeh.dk/2010/02/03/ServiceLocatorisanAnti-Pattern/)
+
+**Hidden Dependencies:**
+- Dependencies are not visible in constructor
+- Makes code harder to understand and test
+- Violates Explicit Dependencies Principle
+- Reference: [DevIQ - Explicit Dependencies](https://deviq.com/principles/explicit-dependencies-principle)
+
+**Testing Difficulties:**
+- Need to set up global locator for tests
+- Tests become coupled to locator setup
+- Reference: [Stack Overflow - Service Locator Testing](https://stackoverflow.com/questions/1557781/is-service-locator-an-anti-pattern)
+
+### Dependency Injection Alternative
+
+**Constructor Injection:**
+- Dependencies declared in constructor
+- Compiler enforces dependency provision
+- Clear, testable code
+- Reference: Already covered in Section 6 - Repository Pattern
+
+**Benefits over Service Locator:**
+- Explicit dependencies
+- Easier testing (just pass mocks)
+- IDE support for navigation
+- Compile-time checking
+- Reference: [Martin Fowler - Constructor Injection](https://martinfowler.com/articles/injection.html#ConstructorInjectionWithPicocontainer)
+
+---
+
+## 25. Double Dispatch and Visitor Pattern
+
+### Gang of Four: Visitor Pattern
+
+**Design Patterns** (1994)
+- Authors: Gang of Four
+- Visitor Pattern chapter
+- "Represent an operation to be performed on the elements of an object structure"
+- Reference: [Wikipedia - Visitor Pattern](https://en.wikipedia.org/wiki/Visitor_pattern)
+
+**Intent:**
+- "Lets you define a new operation without changing the classes of the elements on which it operates"
+- Separates algorithms from object structure
+- Reference: [Refactoring Guru - Visitor](https://refactoring.guru/design-patterns/visitor)
+
+### Double Dispatch Mechanism
+
+**Definition:**
+- "A mechanism that dispatches a function call to different concrete functions depending on the runtime types of two objects involved in the call"
+- Visitor pattern uses double dispatch
+- Reference: [Wikipedia - Double Dispatch](https://en.wikipedia.org/wiki/Double_dispatch)
+
+**How It Works:**
+1. Client calls element.accept(visitor)
+2. Element calls visitor.visit(this) - first dispatch
+3. Correct visit() overload selected - second dispatch
+- Reference: [SourceMaking - Visitor](https://sourcemaking.com/design_patterns/visitor)
+
+### When to Use
+
+**Good Use Cases:**
+- Operations on complex object structures
+- Many distinct operations needed
+- Object structure rarely changes but operations change often
+- Reference: [Refactoring Guru - Visitor Use Cases](https://refactoring.guru/design-patterns/visitor)
+
+**Alternative to Type Checking:**
+- Replace instanceof/typeof checks with polymorphism
+- More maintainable and extensible
+- Reference: [Replace Conditional with Polymorphism](https://refactoring.guru/replace-conditional-with-polymorphism)
+
+### Trade-offs
+
+**Advantages:**
+- Open/Closed Principle for new operations
+- Related operations grouped in one class
+- Accumulate state while traversing
+- Reference: [GoF Design Patterns](https://www.amazon.com/Design-Patterns-Elements-Reusable-Object-Oriented/dp/0201633612)
+
+**Disadvantages:**
+- Adding new element types requires changing all visitors
+- May break encapsulation (visitors need access to element internals)
+- Reference: [C2 Wiki - Visitor Pattern](https://wiki.c2.com/?VisitorPattern)
+
+---
+
+## 26. Entity Identity
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Entity Definition:**
+- "An object that is not defined by its attributes, but rather by a thread of continuity and its identity"
+- "Some objects are not defined primarily by their attributes. They represent a thread of identity"
+- Reference: [Martin Fowler - Evans Classification](https://martinfowler.com/bliki/EvansClassification.html)
+
+**Identity Characteristics:**
+- Unique within the system
+- Stable over time (doesn't change)
+- Survives state changes
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+### Vaughn Vernon: Identity Implementation
+
+**Implementing Domain-Driven Design** (2013)
+- Chapter 5: "Entities"
+- Detailed coverage of identity strategies
+- "The primary characteristic of an Entity is that it has a unique identity"
+- Reference: [Vaughn Vernon - Implementing DDD](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+**Identity Types:**
+- Natural keys (SSN, email)
+- Surrogate keys (UUID, auto-increment)
+- Domain-generated IDs
+- Reference: [Microsoft - Entity Keys](https://learn.microsoft.com/en-us/ef/core/modeling/keys)
+
+### Identity Best Practices
+
+**Immutability of Identity:**
+- Identity should never change after creation
+- Use readonly/final fields
+- Reference: [StackExchange - Mutable Entity ID](https://softwareengineering.stackexchange.com/questions/375765/is-it-bad-practice-to-have-mutable-entity-ids)
+
+**Value Object for Identity:**
+- Wrap identity in Value Object (UserId, OrderId)
+- Type safety prevents mixing IDs
+- Can include validation logic
+- Reference: [Enterprise Craftsmanship - Strongly Typed IDs](https://enterprisecraftsmanship.com/posts/strongly-typed-ids/)
+
+**Equality Based on Identity:**
+- Entity equality should compare only identity
+- Not all attributes
+- Reference: [Vaughn Vernon - Entity Equality](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+---
+
+## 27. Saga Pattern
+
+### Original Research
+
+**Paper: Sagas** (1987)
+- Authors: Hector Garcia-Molina and Kenneth Salem
+- Published: ACM SIGMOD Conference
+- Introduced Sagas for long-lived transactions
+- Reference: [ACM Digital Library - Sagas](https://dl.acm.org/doi/10.1145/38713.38742)
+
+**Definition:**
+- "A saga is a sequence of local transactions where each transaction updates data within a single service"
+- Alternative to distributed transactions
+- Reference: [Microsoft - Saga Pattern](https://learn.microsoft.com/en-us/azure/architecture/reference-architectures/saga/saga)
+
+### Chris Richardson: Microservices Patterns
+
+**Book: Microservices Patterns** (2018)
+- Author: Chris Richardson
+- Publisher: Manning
+- ISBN: 978-1617294549
+- Chapter 4: "Managing Transactions with Sagas"
+- Reference: [Manning - Microservices Patterns](https://www.manning.com/books/microservices-patterns)
+
+**Saga Types:**
+1. **Choreography**: Each service publishes events that trigger next steps
+2. **Orchestration**: Central coordinator tells services what to do
+- Reference: [Microservices.io - Saga](https://microservices.io/patterns/data/saga.html)
+
+### Compensating Transactions
+
+**Core Concept:**
+- Each step has a compensating action to undo it
+- If step N fails, compensate steps N-1, N-2, ..., 1
+- Reference: [AWS - Saga Pattern](https://docs.aws.amazon.com/prescriptive-guidance/latest/modernization-data-persistence/saga-pattern.html)
+
+**Compensation Examples:**
+- CreateOrder → DeleteOrder
+- ReserveInventory → ReleaseInventory
+- ChargePayment → RefundPayment
+- Reference: [Microsoft - Compensating Transactions](https://learn.microsoft.com/en-us/azure/architecture/patterns/compensating-transaction)
+
+### Trade-offs
+
+**Advantages:**
+- Works across service boundaries
+- No distributed locks
+- Services remain autonomous
+- Reference: [Chris Richardson - Saga](https://chrisrichardson.net/post/microservices/patterns/data/2019/07/22/design-sagas.html)
+
+**Challenges:**
+- Complexity of compensation logic
+- Eventual consistency
+- Debugging distributed sagas
+- Reference: [Microsoft - Saga Considerations](https://learn.microsoft.com/en-us/azure/architecture/reference-architectures/saga/saga#issues-and-considerations)
+
+---
+
+## 28. Anti-Corruption Layer
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Original Definition:**
+- Chapter 14: "Maintaining Model Integrity"
+- "Create an isolating layer to provide clients with functionality in terms of their own domain model"
+- Protects your model from external/legacy models
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+**Purpose:**
+- "The translation layer between a new system and an external system"
+- Prevents external model concepts from leaking in
+- Reference: [Martin Fowler - Anti-Corruption Layer](https://martinfowler.com/bliki/AntiCorruptionLayer.html)
+
+### Microsoft Guidance
+
+**Azure Architecture Center:**
+- "Implement a facade or adapter layer between different subsystems that don't share the same semantics"
+- Isolate subsystems by placing an anti-corruption layer between them
+- Reference: [Microsoft - ACL Pattern](https://learn.microsoft.com/en-us/azure/architecture/patterns/anti-corruption-layer)
+
+**When to Use:**
+- Integrating with legacy systems
+- Migrating from monolith to microservices
+- Working with third-party APIs
+- Reference: [Microsoft - ACL When to Use](https://learn.microsoft.com/en-us/azure/architecture/patterns/anti-corruption-layer#when-to-use-this-pattern)
+
+### Components of ACL
+
+**Facade:**
+- Simplified interface to external system
+- Hides complexity from domain
+- Reference: [Refactoring Guru - Facade](https://refactoring.guru/design-patterns/facade)
+
+**Adapter:**
+- Translates between interfaces
+- Maps external model to domain model
+- Reference: [Refactoring Guru - Adapter](https://refactoring.guru/design-patterns/adapter)
+
+**Translator:**
+- Converts data structures
+- Maps field names and types
+- Handles semantic differences
+- Reference: [Evans DDD - Model Translation](https://www.domainlanguage.com/)
+
+### Benefits
+
+**Isolation:**
+- Changes to external system don't ripple through domain
+- Domain model remains pure
+- Reference: [Microsoft - ACL Benefits](https://learn.microsoft.com/en-us/azure/architecture/patterns/anti-corruption-layer)
+
+**Gradual Migration:**
+- Replace legacy components incrementally
+- Strangler Fig pattern compatibility
+- Reference: [Martin Fowler - Strangler Fig](https://martinfowler.com/bliki/StranglerFigApplication.html)
+
+---
+
+## 29. Ubiquitous Language
+
+### Eric Evans: Domain-Driven Design (2003)
+
+**Original Definition:**
+- Chapter 2: "Communication and the Use of Language"
+- "A language structured around the domain model and used by all team members"
+- "The vocabulary of that Ubiquitous Language includes the names of classes and prominent operations"
+- Reference: [Martin Fowler - Ubiquitous Language](https://martinfowler.com/bliki/UbiquitousLanguage.html)
+
+**Key Principles:**
+- Shared by developers and domain experts
+- Used in code, conversations, and documentation
+- Changes to language reflect model changes
+- Reference: [DDD Reference](https://www.domainlanguage.com/wp-content/uploads/2016/05/DDD_Reference_2015-03.pdf)
+
+### Why It Matters
+
+**Communication Benefits:**
+- Reduces translation between business and tech
+- Catches misunderstandings early
+- Domain experts can read code names
+- Reference: [InfoQ - Ubiquitous Language](https://www.infoq.com/articles/ddd-ubiquitous-language/)
+
+**Design Benefits:**
+- Model reflects real domain concepts
+- Code becomes self-documenting
+- Easier onboarding for new team members
+- Reference: [Vaughn Vernon - Implementing DDD](https://www.amazon.com/Implementing-Domain-Driven-Design-Vaughn-Vernon/dp/0321834577)
+
+### Building Ubiquitous Language
+
+**Glossary:**
+- Document key terms and definitions
+- Keep updated as understanding evolves
+- Reference: [DDD Community - Glossary](https://thedomaindrivendesign.io/glossary/)
+
+**Event Storming:**
+- Collaborative workshop technique
+- Discover domain events and concepts
+- Build shared understanding and language
+- Reference: [Alberto Brandolini - Event Storming](https://www.eventstorming.com/)
+
+### Common Pitfalls
+
+**Inconsistent Terminology:**
+- Same concept with different names (Customer/Client/User)
+- Different concepts with same name
+- Reference: [Domain Language - Building UL](https://www.domainlanguage.com/)
+
+**Technical Terms in Domain:**
+- "DTO", "Entity", "Repository" are technical
+- Domain should use business terms
+- Reference: [Evans DDD - Model-Driven Design](https://www.domainlanguage.com/)
+
+---
+
 ## Conclusion
 
 The code quality detection rules implemented in Guardian are firmly grounded in:
 
-1. **Academic Research**: Peer-reviewed papers on software maintainability, complexity metrics, code quality, technical debt prioritization, and severity classification
+1. **Academic Research**: Peer-reviewed papers on software maintainability, complexity metrics, code quality, technical debt prioritization, severity classification, and distributed systems (Sagas)
 2. **Industry Standards**: ISO/IEC 25010, SonarQube rules, OWASP security guidelines, Google and Airbnb style guides
 3. **Authoritative Books**:
+   - Gang of Four's "Design Patterns" (1994)
+   - Bertrand Meyer's "Object-Oriented Software Construction" (1988, 1997)
    - Robert C. Martin's "Clean Architecture" (2017)
    - Vaughn Vernon's "Implementing Domain-Driven Design" (2013)
+   - Chris Richardson's "Microservices Patterns" (2018)
    - Eric Evans' "Domain-Driven Design" (2003)
    - Martin Fowler's "Patterns of Enterprise Application Architecture" (2002)
    - Martin Fowler's "Refactoring" (1999, 2018)
    - Steve McConnell's "Code Complete" (1993, 2004)
-4. **Expert Guidance**: Martin Fowler, Robert C. Martin (Uncle Bob), Eric Evans, Vaughn Vernon, Alistair Cockburn, Kent Beck
+   - Joshua Bloch's "Effective Java" (2001, 2018)
+   - Mark Seemann's "Dependency Injection in .NET" (2011, 2019)
+   - Bobby Woolf's "Null Object" in PLoPD3 (1997)
+4. **Expert Guidance**: Martin Fowler, Robert C. Martin (Uncle Bob), Eric Evans, Vaughn Vernon, Alistair Cockburn, Kent Beck, Greg Young, Bertrand Meyer, Mark Seemann, Chris Richardson, Alberto Brandolini
 5. **Security Standards**: OWASP Secrets Management, GitHub Secret Scanning, GitGuardian best practices
 6. **Open Source Tools**: ArchUnit, SonarQube, ESLint, Secretlint - widely adopted in enterprise environments
+7. **DDD Tactical & Strategic Patterns**: Domain Events, Value Objects, Entities, Aggregates, Bounded Contexts, Anti-Corruption Layer, Ubiquitous Language, Specifications, Factories
+8. **Architectural Patterns**: CQS/CQRS, Saga, Visitor/Double Dispatch, Null Object, Persistence Ignorance
 
 These rules represent decades of software engineering wisdom, empirical research, security best practices, and battle-tested practices from the world's leading software organizations and thought leaders.
 
@@ -845,9 +1678,9 @@ These rules represent decades of software engineering wisdom, empirical research
 
 ---
 
-**Document Version**: 1.1
-**Last Updated**: 2025-11-26
+**Document Version**: 2.0
+**Last Updated**: 2025-12-04
 **Questions or want to contribute research?**
 - 📧 Email: fozilbek.samiyev@gmail.com
 - 🐙 GitHub: https://github.com/samiyev/puaros/issues
-**Based on research as of**: November 2025
+**Based on research as of**: December 2025

packages/ipuaro/ARCHITECTURE.md

@@ -0,0 +1,566 @@
+# ipuaro Architecture
+
+This document describes the architecture, design decisions, and implementation details of ipuaro.
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Clean Architecture](#clean-architecture)
+- [Layer Details](#layer-details)
+- [Data Flow](#data-flow)
+- [Key Design Decisions](#key-design-decisions)
+- [Tech Stack](#tech-stack)
+- [Performance Considerations](#performance-considerations)
+
+## Overview
+
+ipuaro is a local AI agent for codebase operations built on Clean Architecture principles. It enables "infinite" context feeling through lazy loading and AST-based code understanding.
+
+### Core Concepts
+
+1. **Lazy Loading**: Load code on-demand via tools, not all at once
+2. **AST-Based Understanding**: Parse and index code structure for fast lookups
+3. **100% Local**: Ollama LLM + Redis storage, no cloud dependencies
+4. **Session Persistence**: Resume conversations across restarts
+5. **Tool-Based Interface**: LLM accesses code through 18 specialized tools
+
+## Clean Architecture
+
+The project follows Clean Architecture with strict dependency rules:
+
+```
+┌─────────────────────────────────────────────────┐
+│                     TUI Layer                    │  ← Ink/React components
+│                   (Framework)                    │
+├─────────────────────────────────────────────────┤
+│                   CLI Layer                      │  ← Commander.js entry
+│                  (Interface)                     │
+├─────────────────────────────────────────────────┤
+│              Infrastructure Layer                │  ← External adapters
+│  (Storage, LLM, Indexer, Tools, Security)       │
+├─────────────────────────────────────────────────┤
+│              Application Layer                   │  ← Use cases & DTOs
+│     (StartSession, HandleMessage, etc.)          │
+├─────────────────────────────────────────────────┤
+│                 Domain Layer                     │  ← Business logic
+│  (Entities, Value Objects, Service Interfaces)  │
+└─────────────────────────────────────────────────┘
+```
+
+**Dependency Rule**: Outer layers depend on inner layers, never the reverse.
+
+## Layer Details
+
+### Domain Layer (Core Business Logic)
+
+**Location**: `src/domain/`
+
+**Responsibilities**:
+- Define business entities and value objects
+- Declare service interfaces (ports)
+- No external dependencies (pure TypeScript)
+
+**Components**:
+
+```
+domain/
+├── entities/
+│   ├── Session.ts           # Session entity with history and stats
+│   └── Project.ts           # Project entity with metadata
+├── value-objects/
+│   ├── FileData.ts          # File content with hash and size
+│   ├── FileAST.ts           # Parsed AST structure
+│   ├── FileMeta.ts          # Complexity, dependencies, hub detection
+│   ├── ChatMessage.ts       # Message with role, content, tool calls
+│   ├── ToolCall.ts          # Tool invocation with parameters
+│   ├── ToolResult.ts        # Tool execution result
+│   └── UndoEntry.ts         # File change for undo stack
+├── services/
+│   ├── IStorage.ts          # Storage interface (port)
+│   ├── ILLMClient.ts        # LLM interface (port)
+│   ├── ITool.ts             # Tool interface (port)
+│   └── IIndexer.ts          # Indexer interface (port)
+└── constants/
+    └── index.ts             # Domain constants
+```
+
+**Key Design**:
+- Value objects are immutable
+- Entities have identity and lifecycle
+- Interfaces define contracts, not implementations
+
+### Application Layer (Use Cases)
+
+**Location**: `src/application/`
+
+**Responsibilities**:
+- Orchestrate domain logic
+- Implement use cases (application-specific business rules)
+- Define DTOs for data transfer
+- Coordinate between domain and infrastructure
+
+**Components**:
+
+```
+application/
+├── use-cases/
+│   ├── StartSession.ts      # Initialize or load session
+│   ├── HandleMessage.ts     # Main message orchestrator
+│   ├── IndexProject.ts      # Project indexing workflow
+│   ├── ExecuteTool.ts       # Tool execution with validation
+│   └── UndoChange.ts        # Revert file changes
+├── dtos/
+│   ├── SessionDto.ts        # Session data transfer object
+│   ├── MessageDto.ts        # Message DTO
+│   └── ToolCallDto.ts       # Tool call DTO
+├── mappers/
+│   └── SessionMapper.ts     # Domain ↔ DTO conversion
+└── interfaces/
+    └── IToolRegistry.ts     # Tool registry interface
+```
+
+**Key Use Cases**:
+
+1. **StartSession**: Creates new session or loads latest
+2. **HandleMessage**: Main flow (LLM → Tools → Response)
+3. **IndexProject**: Scan → Parse → Analyze → Store
+4. **UndoChange**: Restore file from undo stack
+
+### Infrastructure Layer (External Implementations)
+
+**Location**: `src/infrastructure/`
+
+**Responsibilities**:
+- Implement domain interfaces
+- Handle external systems (Redis, Ollama, filesystem)
+- Provide concrete tool implementations
+- Security and validation
+
+**Components**:
+
+```
+infrastructure/
+├── storage/
+│   ├── RedisClient.ts       # Redis connection wrapper
+│   ├── RedisStorage.ts      # IStorage implementation
+│   └── schema.ts            # Redis key schema
+├── llm/
+│   ├── OllamaClient.ts      # ILLMClient implementation
+│   ├── prompts.ts           # System prompts
+│   └── ResponseParser.ts    # Parse XML tool calls
+├── indexer/
+│   ├── FileScanner.ts       # Recursive file scanning
+│   ├── ASTParser.ts         # tree-sitter parsing
+│   ├── MetaAnalyzer.ts      # Complexity and dependencies
+│   ├── IndexBuilder.ts      # Symbol index + deps graph
+│   └── Watchdog.ts          # File watching (chokidar)
+├── tools/                   # 18 tool implementations
+│   ├── registry.ts
+│   ├── read/                # GetLines, GetFunction, GetClass, GetStructure
+│   ├── edit/                # EditLines, CreateFile, DeleteFile
+│   ├── search/              # FindReferences, FindDefinition
+│   ├── analysis/            # GetDependencies, GetDependents, GetComplexity, GetTodos
+│   ├── git/                 # GitStatus, GitDiff, GitCommit
+│   └── run/                 # RunCommand, RunTests
+└── security/
+    ├── Blacklist.ts         # Dangerous commands
+    ├── Whitelist.ts         # Safe commands
+    └── PathValidator.ts     # Path traversal prevention
+```
+
+**Key Implementations**:
+
+1. **RedisStorage**: Uses Redis hashes for files/AST/meta, lists for undo
+2. **OllamaClient**: HTTP API client with tool calling support
+3. **ASTParser**: tree-sitter for TS/JS/TSX/JSX parsing
+4. **ToolRegistry**: Manages tool lifecycle and execution
+
+### TUI Layer (Terminal UI)
+
+**Location**: `src/tui/`
+
+**Responsibilities**:
+- Render terminal UI with Ink (React for terminal)
+- Handle user input and hotkeys
+- Display chat history and status
+
+**Components**:
+
+```
+tui/
+├── App.tsx                  # Main app shell
+├── components/
+│   ├── StatusBar.tsx        # Top status bar
+│   ├── Chat.tsx             # Message history display
+│   ├── Input.tsx            # User input with history
+│   ├── DiffView.tsx         # Inline diff display
+│   ├── ConfirmDialog.tsx    # Edit confirmation
+│   ├── ErrorDialog.tsx      # Error handling
+│   └── Progress.tsx         # Progress bar (indexing)
+└── hooks/
+    ├── useSession.ts        # Session state management
+    ├── useHotkeys.ts        # Keyboard shortcuts
+    └── useCommands.ts       # Slash command handling
+```
+
+**Key Features**:
+
+- Real-time status updates (context usage, session time)
+- Input history with ↑/↓ navigation
+- Hotkeys: Ctrl+C (interrupt), Ctrl+D (exit), Ctrl+Z (undo)
+- Diff preview for edits with confirmation
+- Error recovery with retry/skip/abort options
+
+### CLI Layer (Entry Point)
+
+**Location**: `src/cli/`
+
+**Responsibilities**:
+- Command-line interface with Commander.js
+- Dependency injection and initialization
+- Onboarding checks (Redis, Ollama, model)
+
+**Components**:
+
+```
+cli/
+├── index.ts                 # Commander.js setup
+└── commands/
+    ├── start.ts             # Start TUI (default command)
+    ├── init.ts              # Create .ipuaro.json config
+    └── index-cmd.ts         # Index-only command
+```
+
+**Commands**:
+
+1. `ipuaro [path]` - Start TUI in directory
+2. `ipuaro init` - Create config file
+3. `ipuaro index` - Index without TUI
+
+### Shared Module
+
+**Location**: `src/shared/`
+
+**Responsibilities**:
+- Cross-cutting concerns
+- Configuration management
+- Error handling
+- Utility functions
+
+**Components**:
+
+```
+shared/
+├── types/
+│   └── index.ts             # Shared TypeScript types
+├── constants/
+│   ├── config.ts            # Config schema and loader
+│   └── messages.ts          # User-facing messages
+├── utils/
+│   ├── hash.ts              # MD5 hashing
+│   └── tokens.ts            # Token estimation
+└── errors/
+    ├── IpuaroError.ts       # Custom error class
+    └── ErrorHandler.ts      # Error handling service
+```
+
+## Data Flow
+
+### 1. Startup Flow
+
+```
+CLI Entry (bin/ipuaro.js)
+    ↓
+Commander.js parses arguments
+    ↓
+Onboarding checks (Redis, Ollama, Model)
+    ↓
+Initialize dependencies:
+    - RedisClient connects
+    - RedisStorage initialized
+    - OllamaClient created
+    - ToolRegistry with 18 tools
+    ↓
+StartSession use case:
+    - Load latest session or create new
+    - Initialize ContextManager
+    ↓
+Launch TUI (App.tsx)
+    - Render StatusBar, Chat, Input
+    - Set up hotkeys
+```
+
+### 2. Message Flow
+
+```
+User types message in Input.tsx
+    ↓
+useSession.handleMessage()
+    ↓
+HandleMessage use case:
+    1. Add user message to history
+    2. Build context (system prompt + structure + AST)
+    3. Send to OllamaClient.chat()
+    4. Parse tool calls from response
+    5. For each tool call:
+        - If requiresConfirmation: show ConfirmDialog
+        - Execute tool via ToolRegistry
+        - Collect results
+    6. If tool results: goto step 3 (continue loop)
+    7. Add assistant response to history
+    8. Update session in Redis
+    ↓
+Display response in Chat.tsx
+```
+
+### 3. Edit Flow
+
+```
+LLM calls edit_lines tool
+    ↓
+ToolRegistry.execute()
+    ↓
+EditLinesTool.execute():
+    1. Validate path (PathValidator)
+    2. Check hash conflict
+    3. Build diff
+    ↓
+ConfirmDialog shows diff
+    ↓
+User chooses:
+    - Apply: Continue
+    - Cancel: Return error to LLM
+    - Edit: Manual edit (future)
+    ↓
+If Apply:
+    1. Create UndoEntry
+    2. Push to undo stack (Redis list)
+    3. Write to filesystem
+    4. Update RedisStorage (lines, hash, AST, meta)
+    ↓
+Return success to LLM
+```
+
+### 4. Indexing Flow
+
+```
+FileScanner.scan()
+    - Recursively walk directory
+    - Filter via .gitignore + ignore patterns
+    - Detect binary files (skip)
+    ↓
+For each file:
+    ASTParser.parse()
+        - tree-sitter parse
+        - Extract imports, exports, functions, classes
+        ↓
+    MetaAnalyzer.analyze()
+        - Calculate complexity (LOC, nesting, cyclomatic)
+        - Resolve dependencies (imports → file paths)
+        - Detect hubs (>5 dependents)
+        ↓
+    RedisStorage.setFile(), .setAST(), .setMeta()
+    ↓
+IndexBuilder.buildSymbolIndex()
+    - Map symbol names → locations
+    ↓
+IndexBuilder.buildDepsGraph()
+    - Build bidirectional import graph
+    ↓
+Store indexes in Redis
+    ↓
+Watchdog.start()
+    - Watch for file changes
+    - On change: Re-parse and update indexes
+```
+
+## Key Design Decisions
+
+### 1. Why Redis?
+
+**Pros**:
+- Fast in-memory access for frequent reads
+- AOF persistence (append-only file) for durability
+- Native support for hashes, lists, sets
+- Simple key-value model fits our needs
+- Excellent for session data
+
+**Alternatives considered**:
+- SQLite: Slower, overkill for our use case
+- JSON files: No concurrent access, slow for large data
+- PostgreSQL: Too heavy, we don't need relational features
+
+### 2. Why tree-sitter?
+
+**Pros**:
+- Incremental parsing (fast re-parsing)
+- Error-tolerant (works with syntax errors)
+- Multi-language support
+- Used by GitHub, Neovim, Atom
+
+**Alternatives considered**:
+- TypeScript Compiler API: TS-only, not error-tolerant
+- Babel: JS-focused, heavy dependencies
+- Regex: Fragile, inaccurate
+
+### 3. Why Ollama?
+
+**Pros**:
+- 100% local, no API keys
+- Easy installation (brew install ollama)
+- Good model selection (qwen2.5-coder, deepseek-coder)
+- Tool calling support
+
+**Alternatives considered**:
+- OpenAI: Costs money, sends code to cloud
+- Anthropic Claude: Same concerns as OpenAI
+- llama.cpp: Lower level, requires more setup
+
+Planned: Support for OpenAI/Anthropic in v1.2.0 as optional providers.
+
+### 4. Why XML for Tool Calls?
+
+**Pros**:
+- LLMs trained on XML (very common format)
+- Self-describing (parameter names in tags)
+- Easy to parse with regex
+- More reliable than JSON for smaller models
+
+**Alternatives considered**:
+- JSON: Smaller models struggle with exact JSON syntax
+- Function calling API: Not all models support it
+
+### 5. Why Clean Architecture?
+
+**Pros**:
+- Testability (domain has no external dependencies)
+- Flexibility (easy to swap Redis for SQLite)
+- Maintainability (clear separation of concerns)
+- Scalability (layers can evolve independently)
+
+**Cost**: More files and indirection, but worth it for long-term maintenance.
+
+### 6. Why Lazy Loading Instead of RAG?
+
+**RAG (Retrieval Augmented Generation)**:
+- Pre-computes embeddings
+- Searches embeddings for relevant chunks
+- Adds chunks to context
+
+**Lazy Loading (our approach)**:
+- Agent requests specific code via tools
+- More precise control over what's loaded
+- Simpler implementation (no embeddings)
+- Works with any LLM (no embedding model needed)
+
+**Trade-off**: RAG might be better for semantic search ("find error handling code"), but tool-based approach gives agent explicit control.
+
+## Tech Stack
+
+### Core Dependencies
+
+| Package | Purpose | Why? |
+|---------|---------|------|
+| `ioredis` | Redis client | Most popular, excellent TypeScript support |
+| `ollama` | LLM client | Official SDK, simple API |
+| `tree-sitter` | AST parsing | Fast, error-tolerant, multi-language |
+| `tree-sitter-typescript` | TS/TSX parser | Official TypeScript grammar |
+| `tree-sitter-javascript` | JS/JSX parser | Official JavaScript grammar |
+| `ink` | Terminal UI | React for terminal, declarative |
+| `ink-text-input` | Input component | Maintained ink component |
+| `react` | UI framework | Required by Ink |
+| `simple-git` | Git operations | Simple API, well-tested |
+| `chokidar` | File watching | Cross-platform, reliable |
+| `commander` | CLI framework | Industry standard |
+| `zod` | Validation | Type-safe validation |
+| `globby` | File globbing | ESM-native, .gitignore support |
+
+### Development Dependencies
+
+| Package | Purpose |
+|---------|---------|
+| `vitest` | Testing framework |
+| `@vitest/coverage-v8` | Coverage reporting |
+| `@vitest/ui` | Interactive test UI |
+| `tsup` | TypeScript bundler |
+| `typescript` | Type checking |
+
+## Performance Considerations
+
+### 1. Indexing Performance
+
+**Problem**: Large projects (10k+ files) take time to index.
+
+**Optimizations**:
+- Incremental parsing with tree-sitter (only changed files)
+- Parallel parsing (planned for v1.1.0)
+- Ignore patterns (.gitignore, node_modules, dist)
+- Skip binary files early
+
+**Current**: ~1000 files/second on M1 Mac
+
+### 2. Memory Usage
+
+**Problem**: Entire AST in memory could be 100s of MB.
+
+**Optimizations**:
+- Store ASTs in Redis (out of Node.js heap)
+- Load ASTs on-demand from Redis
+- Lazy-load file content (not stored in session)
+
+**Current**: ~200MB for 5000 files indexed
+
+### 3. Context Window Management
+
+**Problem**: 128k token context window fills up.
+
+**Optimizations**:
+- Auto-compression at 80% usage
+- LLM summarizes old messages
+- Remove tool results older than 5 messages
+- Only load structure + metadata initially (~10k tokens)
+
+### 4. Redis Performance
+
+**Problem**: Redis is single-threaded.
+
+**Optimizations**:
+- Pipeline commands where possible
+- Use hashes for related data (fewer keys)
+- AOF every second (not every command)
+- Keep undo stack limited (10 entries)
+
+**Current**: <1ms latency for most operations
+
+### 5. Tool Execution
+
+**Problem**: Tool execution could block LLM.
+
+**Current**: Synchronous execution (simpler)
+
+**Future**: Async tool execution with progress callbacks (v1.1.0)
+
+## Future Improvements
+
+### v1.1.0 - Performance
+- Parallel AST parsing
+- Incremental indexing (only changed files)
+- Response caching
+- Stream LLM responses
+
+### v1.2.0 - Features
+- Multiple file edits in one operation
+- Batch operations
+- Custom prompt templates
+- OpenAI/Anthropic provider support
+
+### v1.3.0 - Extensibility
+- Plugin system for custom tools
+- LSP integration
+- Multi-language support (Python, Go, Rust)
+- Custom indexing rules
+
+---
+
+**Last Updated**: 2025-12-01
+**Version**: 0.16.0

packages/ipuaro/README.md

@@ -7,9 +7,9 @@
 [![npm version](https://badge.fury.io/js/@samiyev%2Fipuaro.svg)](https://www.npmjs.com/package/@samiyev/ipuaro)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-> **Status:** 🚧 Early Development (v0.1.0 Foundation)
+> **Status:** 🎉 Release Candidate (v0.16.0 → v1.0.0)
 >
-> Core infrastructure is ready. Active development in progress.
+> All core features complete. Production-ready release coming soon.
 
 ## Vision
 
@@ -19,18 +19,20 @@ Work with codebases of any size using local AI:
 - 🔒 **100% Local**: Your code never leaves your machine
 - ⚡ **Fast**: Redis persistence + tree-sitter parsing
 
-## Planned Features
+## Features
 
-### 18 LLM Tools
+### 18 LLM Tools (All Implemented ✅)
 
-| Category | Tools | Status |
-|----------|-------|--------|
-| **Read** | `get_lines`, `get_function`, `get_class`, `get_structure` | 🔜 v0.5.0 |
-| **Edit** | `edit_lines`, `create_file`, `delete_file` | 🔜 v0.6.0 |
-| **Search** | `find_references`, `find_definition` | 🔜 v0.7.0 |
-| **Analysis** | `get_dependencies`, `get_dependents`, `get_complexity`, `get_todos` | 🔜 v0.8.0 |
-| **Git** | `git_status`, `git_diff`, `git_commit` | 🔜 v0.9.0 |
-| **Run** | `run_command`, `run_tests` | 🔜 v0.9.0 |
+| Category | Tools | Description |
+|----------|-------|-------------|
+| **Read** | `get_lines`, `get_function`, `get_class`, `get_structure` | Read code without loading everything into context |
+| **Edit** | `edit_lines`, `create_file`, `delete_file` | Make changes with confirmation and undo support |
+| **Search** | `find_references`, `find_definition` | Find symbol definitions and usages across codebase |
+| **Analysis** | `get_dependencies`, `get_dependents`, `get_complexity`, `get_todos` | Analyze code structure, complexity, and TODOs |
+| **Git** | `git_status`, `git_diff`, `git_commit` | Git operations with safety checks |
+| **Run** | `run_command`, `run_tests` | Execute commands and tests with security validation |
+
+See [Tools Documentation](#tools-reference) below for detailed usage examples.
 
 ### Terminal UI
 
@@ -54,6 +56,31 @@ Work with codebases of any size using local AI:
 └───────────────────────────────────────────────────────────┘
 ```
 
+### Slash Commands
+
+Control your session with built-in commands:
+
+| Command | Description |
+|---------|-------------|
+| `/help` | Show all commands and hotkeys |
+| `/clear` | Clear chat history (keeps session) |
+| `/undo` | Revert last file change from undo stack |
+| `/sessions [list\|load\|delete] [id]` | Manage sessions |
+| `/status` | Show system status (LLM, context, stats) |
+| `/reindex` | Force full project reindexation |
+| `/eval` | LLM self-check for hallucinations |
+| `/auto-apply [on\|off]` | Toggle auto-apply mode for edits |
+
+### Hotkeys
+
+| Hotkey | Action |
+|--------|--------|
+| `Ctrl+C` | Interrupt generation (1st press) / Exit (2nd press within 1s) |
+| `Ctrl+D` | Exit and save session |
+| `Ctrl+Z` | Undo last file change |
+| `↑` / `↓` | Navigate input history |
+| `Tab` | Path autocomplete (coming soon) |
+
 ### Key Capabilities
 
 🔍 **Smart Code Understanding**
@@ -124,6 +151,23 @@ ipuaro --model qwen2.5-coder:32b-instruct
 ipuaro --auto-apply
 ```
 
+## Quick Start
+
+Try ipuaro with our demo project:
+
+```bash
+# Navigate to demo project
+cd examples/demo-project
+
+# Install dependencies
+npm install
+
+# Start ipuaro
+npx @samiyev/ipuaro
+```
+
+See [examples/demo-project](./examples/demo-project) for detailed usage guide and example conversations.
+
 ## Commands
 
 | Command | Description |
@@ -181,49 +225,263 @@ Clean Architecture with clear separation:
 
 ## Development Status
 
-### ✅ Completed (v0.1.0)
+### ✅ Completed (v0.1.0 - v0.16.0)
 
-- [x] Project setup (tsup, vitest, ESM)
-- [x] Domain entities (Session, Project)
-- [x] Value objects (FileData, FileAST, ChatMessage, etc.)
-- [x] Service interfaces (IStorage, ILLMClient, ITool, IIndexer)
-- [x] Shared module (Config, Errors, Utils)
-- [x] CLI placeholder commands
-- [x] 91 unit tests, 100% coverage
+- [x] **v0.1.0 - v0.4.0**: Foundation (domain, storage, indexer, LLM integration)
+- [x] **v0.5.0 - v0.9.0**: All 18 tools implemented
+- [x] **v0.10.0**: Session management with undo support
+- [x] **v0.11.0 - v0.12.0**: Full TUI with all components
+- [x] **v0.13.0**: Security (PathValidator, command validation)
+- [x] **v0.14.0**: 8 slash commands
+- [x] **v0.15.0**: CLI entry point with onboarding
+- [x] **v0.16.0**: Comprehensive error handling system
+- [x] **1420 tests, 98% coverage**
 
-### 🔜 Next Up
+### 🔜 v1.0.0 - Production Ready
 
-- [ ] **v0.2.0** - Redis Storage
-- [ ] **v0.3.0** - Indexer (file scanning, AST parsing)
-- [ ] **v0.4.0** - LLM Integration (Ollama)
-- [ ] **v0.5.0-0.9.0** - Tools implementation
-- [ ] **v0.10.0** - Session management
-- [ ] **v0.11.0** - TUI
+- [ ] Performance optimizations
+- [ ] Complete documentation
+- [ ] Working examples
 
-See [ROADMAP.md](./ROADMAP.md) for detailed development plan.
+See [ROADMAP.md](./ROADMAP.md) for detailed development plan and [CHANGELOG.md](./CHANGELOG.md) for release history.
 
-## API (Coming Soon)
+## Tools Reference
+
+The AI agent has access to 18 tools for working with your codebase. Here are the most commonly used ones:
+
+### Read Tools
+
+**`get_lines(path, start?, end?)`**
+Read specific lines from a file.
+
+```
+You: Show me the authentication logic
+Assistant: [get_lines src/auth/service.ts 45 67]
+# Returns lines 45-67 with line numbers
+```
+
+**`get_function(path, name)`**
+Get a specific function's source code and metadata.
+
+```
+You: How does the login function work?
+Assistant: [get_function src/auth/service.ts login]
+# Returns function code, params, return type, and metadata
+```
+
+**`get_class(path, name)`**
+Get a specific class's source code and metadata.
+
+```
+You: Show me the UserService class
+Assistant: [get_class src/services/user.ts UserService]
+# Returns class code, methods, properties, and inheritance info
+```
+
+**`get_structure(path?, depth?)`**
+Get directory tree structure.
+
+```
+You: What's in the src/auth directory?
+Assistant: [get_structure src/auth]
+# Returns ASCII tree with files and folders
+```
+
+### Edit Tools
+
+**`edit_lines(path, start, end, content)`**
+Replace lines in a file (requires confirmation).
+
+```
+You: Update the timeout to 5000ms
+Assistant: [edit_lines src/config.ts 23 23 "  timeout: 5000,"]
+# Shows diff, asks for confirmation
+```
+
+**`create_file(path, content)`**
+Create a new file (requires confirmation).
+
+```
+You: Create a new utility for date formatting
+Assistant: [create_file src/utils/date.ts "export function formatDate..."]
+# Creates file after confirmation
+```
+
+**`delete_file(path)`**
+Delete a file (requires confirmation).
+
+```
+You: Remove the old test file
+Assistant: [delete_file tests/old-test.test.ts]
+# Deletes after confirmation
+```
+
+### Search Tools
+
+**`find_references(symbol, path?)`**
+Find all usages of a symbol across the codebase.
+
+```
+You: Where is getUserById used?
+Assistant: [find_references getUserById]
+# Returns all files/lines where it's called
+```
+
+**`find_definition(symbol)`**
+Find where a symbol is defined.
+
+```
+You: Where is ApiClient defined?
+Assistant: [find_definition ApiClient]
+# Returns file, line, and context
+```
+
+### Analysis Tools
+
+**`get_dependencies(path)`**
+Get files that a specific file imports.
+
+```
+You: What does auth.ts depend on?
+Assistant: [get_dependencies src/auth/service.ts]
+# Returns list of imported files
+```
+
+**`get_dependents(path)`**
+Get files that import a specific file.
+
+```
+You: What files use the database module?
+Assistant: [get_dependents src/db/index.ts]
+# Returns list of files importing this
+```
+
+**`get_complexity(path?, limit?)`**
+Get complexity metrics for files.
+
+```
+You: Which files are most complex?
+Assistant: [get_complexity null 10]
+# Returns top 10 most complex files with metrics
+```
+
+**`get_todos(path?, type?)`**
+Find TODO/FIXME/HACK comments.
+
+```
+You: What TODOs are there?
+Assistant: [get_todos]
+# Returns all TODO comments with locations
+```
+
+### Git Tools
+
+**`git_status()`**
+Get current git repository status.
+
+```
+You: What files have changed?
+Assistant: [git_status]
+# Returns branch, staged, modified, untracked files
+```
+
+**`git_diff(path?, staged?)`**
+Get uncommitted changes.
+
+```
+You: Show me what changed in auth.ts
+Assistant: [git_diff src/auth/service.ts]
+# Returns diff output
+```
+
+**`git_commit(message, files?)`**
+Create a git commit (requires confirmation).
+
+```
+You: Commit these auth changes
+Assistant: [git_commit "feat: add password reset flow" ["src/auth/service.ts"]]
+# Creates commit after confirmation
+```
+
+### Run Tools
+
+**`run_command(command, timeout?)`**
+Execute shell commands (with security validation).
+
+```
+You: Run the build
+Assistant: [run_command "npm run build"]
+# Checks security, then executes
+```
+
+**`run_tests(path?, filter?, watch?)`**
+Run project tests.
+
+```
+You: Test the auth module
+Assistant: [run_tests "tests/auth" null false]
+# Auto-detects test runner and executes
+```
+
+For complete tool documentation with all parameters and options, see [TOOLS.md](./TOOLS.md).
+
+## Programmatic API
+
+You can use ipuaro as a library in your own Node.js applications:
 
 ```typescript
-import { startSession, handleMessage } from "@samiyev/ipuaro"
+import {
+    createRedisClient,
+    RedisStorage,
+    OllamaClient,
+    ToolRegistry,
+    StartSession,
+    HandleMessage
+} from "@samiyev/ipuaro"
+
+// Initialize dependencies
+const redis = await createRedisClient({ host: "localhost", port: 6379 })
+const storage = new RedisStorage(redis, "my-project")
+const llm = new OllamaClient({
+    model: "qwen2.5-coder:7b-instruct",
+    contextWindow: 128000,
+    temperature: 0.1
+})
+const tools = new ToolRegistry()
+
+// Register tools
+tools.register(new GetLinesTool(storage, "/path/to/project"))
+// ... register other tools
 
 // Start a session
-const session = await startSession({
-    projectPath: "./my-project",
-    model: "qwen2.5-coder:7b-instruct"
-})
+const startSession = new StartSession(storage)
+const session = await startSession.execute("my-project")
 
-// Send a message
-const response = await handleMessage(session, "Explain the auth flow")
+// Handle a message
+const handleMessage = new HandleMessage(storage, llm, tools)
+await handleMessage.execute(session, "Show me the auth flow")
 
-console.log(response.content)
-console.log(`Tokens: ${response.stats.tokens}`)
-console.log(`Tool calls: ${response.stats.toolCalls}`)
+// Session is automatically updated in Redis
 ```
 
+For full API documentation, see the TypeScript definitions in `src/` or explore the [source code](./src/).
+
 ## How It Works
 
-### Lazy Loading Context
+### 1. Project Indexing
+
+When you start ipuaro, it scans your project and builds an index:
+
+```
+1. File Scanner → Recursively scans files (.ts, .js, .tsx, .jsx)
+2. AST Parser → Parses with tree-sitter (extracts functions, classes, imports)
+3. Meta Analyzer → Calculates complexity, dependencies, hub detection
+4. Index Builder → Creates symbol index and dependency graph
+5. Redis Storage → Persists everything for instant startup next time
+6. Watchdog → Watches files for changes and updates index in background
+```
+
+### 2. Lazy Loading Context
 
 Instead of loading entire codebase into context:
 
@@ -232,24 +490,161 @@ Traditional approach:
 ├── Load all files → 500k tokens → ❌ Exceeds context window
 
 ipuaro approach:
-├── Load project structure → 2k tokens
-├── Load AST metadata → 10k tokens
-├── On demand: get_function("auth.ts", "login") → 200 tokens
-├── Total: ~12k tokens → ✅ Fits in context
+├── Load project structure → ~2k tokens
+├── Load AST metadata → ~10k tokens
+├── On demand: get_function("auth.ts", "login") → ~200 tokens
+├── Total: ~12k tokens → ✅ Fits in 128k context window
 ```
 
-### Tool-Based Code Access
+Context automatically compresses when usage exceeds 80% by summarizing old messages.
+
+### 3. Tool-Based Code Access
+
+The LLM doesn't see your code initially. It only sees structure and metadata. When it needs code, it uses tools:
 
 ```
-User: "How does user creation work?"
+You: "How does user creation work?"
 
-ipuaro:
-1. [get_structure src/] → sees user/ folder
-2. [get_function src/user/service.ts createUser] → gets function code
+Agent reasoning:
+1. [get_structure src/] → sees user/ folder exists
+2. [get_function src/user/service.ts createUser] → loads specific function
 3. [find_references createUser] → finds all usages
-4. Synthesizes answer with specific code context
+4. Synthesizes answer with only relevant code loaded
+
+Total tokens used: ~2k (vs loading entire src/ which could be 50k+)
 ```
 
+### 4. Session Persistence
+
+Everything is saved to Redis:
+- Chat history and context state
+- Undo stack (last 10 file changes)
+- Session metadata and statistics
+
+Resume your session anytime with `/sessions load <id>`.
+
+### 5. Security Model
+
+Three-layer security:
+1. **Blacklist**: Dangerous commands always blocked (rm -rf, sudo, etc.)
+2. **Whitelist**: Safe commands auto-approved (npm, git status, etc.)
+3. **Confirmation**: Unknown commands require user approval
+
+File operations are restricted to project directory only (path traversal prevention).
+
+## Troubleshooting
+
+### Redis Connection Errors
+
+**Error**: `Redis connection failed`
+
+**Solutions**:
+```bash
+# Check if Redis is running
+redis-cli ping  # Should return "PONG"
+
+# Start Redis with AOF persistence
+redis-server --appendonly yes
+
+# Check Redis logs
+tail -f /usr/local/var/log/redis.log  # macOS
+```
+
+### Ollama Model Not Found
+
+**Error**: `Model qwen2.5-coder:7b-instruct not found`
+
+**Solutions**:
+```bash
+# Pull the model
+ollama pull qwen2.5-coder:7b-instruct
+
+# List installed models
+ollama list
+
+# Check Ollama is running
+ollama serve
+```
+
+### Large Project Performance
+
+**Issue**: Indexing takes too long or uses too much memory
+
+**Solutions**:
+```bash
+# Index only a subdirectory
+ipuaro ./src
+
+# Add more ignore patterns to .ipuaro.json
+{
+    "project": {
+        "ignorePatterns": ["node_modules", "dist", ".git", "coverage", "build"]
+    }
+}
+
+# Increase Node.js memory limit
+NODE_OPTIONS="--max-old-space-size=4096" ipuaro
+```
+
+### Context Window Exceeded
+
+**Issue**: `Context window exceeded` errors
+
+**Solutions**:
+- Context auto-compresses at 80%, but you can manually `/clear` history
+- Use more targeted questions instead of asking about entire codebase
+- The agent will automatically use tools to load only what's needed
+
+### File Changes Not Detected
+
+**Issue**: Made changes but agent doesn't see them
+
+**Solutions**:
+```bash
+# Force reindex
+/reindex
+
+# Or restart with fresh index
+rm -rf ~/.ipuaro/cache
+ipuaro
+```
+
+### Undo Not Working
+
+**Issue**: `/undo` says no changes to undo
+
+**Explanation**: Undo stack only tracks the last 10 file edits made through ipuaro. Manual file edits outside ipuaro cannot be undone.
+
+## FAQ
+
+**Q: Does ipuaro send my code to any external servers?**
+
+A: No. Everything runs locally. Ollama runs on your machine, Redis stores data locally, and no network requests are made except to your local Ollama instance.
+
+**Q: What languages are supported?**
+
+A: Currently TypeScript, JavaScript (including TSX/JSX). More languages planned for future versions.
+
+**Q: Can I use OpenAI/Anthropic/other LLM providers?**
+
+A: Currently only Ollama is supported. OpenAI/Anthropic support is planned for v1.2.0.
+
+**Q: How much disk space does Redis use?**
+
+A: Depends on project size. A typical mid-size project (1000 files) uses ~50-100MB. Redis uses AOF persistence, so data survives restarts.
+
+**Q: Can I use ipuaro in a CI/CD pipeline?**
+
+A: Yes, but it's designed for interactive use. For automated code analysis, consider the programmatic API.
+
+**Q: What's the difference between ipuaro and GitHub Copilot?**
+
+A: Copilot is an autocomplete tool. ipuaro is a conversational agent that can read, analyze, modify files, run commands, and has full codebase understanding through AST parsing.
+
+**Q: Why Redis instead of SQLite or JSON files?**
+
+A: Redis provides fast in-memory access, AOF persistence, and handles concurrent access well. The session model fits Redis's data structures perfectly.
+
 ## Contributing
 
 Contributions welcome! This project is in early development.

packages/ipuaro/examples/demo-project/.gitignore

@@ -0,0 +1,4 @@
+node_modules/
+dist/
+*.log
+.DS_Store

packages/ipuaro/examples/demo-project/.ipuaro.json

@@ -0,0 +1,21 @@
+{
+    "redis": {
+        "host": "localhost",
+        "port": 6379
+    },
+    "llm": {
+        "model": "qwen2.5-coder:7b-instruct",
+        "temperature": 0.1
+    },
+    "project": {
+        "ignorePatterns": [
+            "node_modules",
+            "dist",
+            ".git",
+            "*.log"
+        ]
+    },
+    "edit": {
+        "autoApply": false
+    }
+}

packages/ipuaro/examples/demo-project/EXAMPLE_CONVERSATIONS.md

@@ -0,0 +1,8 @@
+# Example Conversations with ipuaro
+
+This document shows realistic conversations you can have with ipuaro when working with the demo project.
+
+## Conversation 1: Understanding the Codebase
+
+```
+You: What does this project do?

packages/ipuaro/examples/demo-project/README.md

@@ -0,0 +1,406 @@
+# ipuaro Demo Project
+
+This is a demo project showcasing ipuaro's capabilities as a local AI agent for codebase operations.
+
+## Project Overview
+
+A simple TypeScript application demonstrating:
+- User management service
+- Authentication service
+- Validation utilities
+- Logging utilities
+- Unit tests
+
+The code intentionally includes various patterns (TODOs, FIXMEs, complex functions, dependencies) to demonstrate ipuaro's analysis tools.
+
+## Setup
+
+### Prerequisites
+
+1. **Redis** - Running locally
+```bash
+# macOS
+brew install redis
+redis-server --appendonly yes
+```
+
+2. **Ollama** - With qwen2.5-coder model
+```bash
+brew install ollama
+ollama serve
+ollama pull qwen2.5-coder:7b-instruct
+```
+
+3. **Node.js** - v20 or higher
+
+### Installation
+
+```bash
+# Install dependencies
+npm install
+
+# Or with pnpm
+pnpm install
+```
+
+## Using ipuaro with Demo Project
+
+### Start ipuaro
+
+```bash
+# From this directory
+npx @samiyev/ipuaro
+
+# Or if installed globally
+ipuaro
+```
+
+### Example Queries
+
+Try these queries to explore ipuaro's capabilities:
+
+#### 1. Understanding the Codebase
+
+```
+You: What is the structure of this project?
+```
+
+ipuaro will use `get_structure` to show the directory tree.
+
+```
+You: How does user creation work?
+```
+
+ipuaro will:
+1. Use `get_structure` to find relevant files
+2. Use `get_function` to read the `createUser` function
+3. Use `find_references` to see where it's called
+4. Explain the flow
+
+#### 2. Finding Issues
+
+```
+You: What TODOs and FIXMEs are in the codebase?
+```
+
+ipuaro will use `get_todos` to list all TODO/FIXME comments.
+
+```
+You: Which files are most complex?
+```
+
+ipuaro will use `get_complexity` to analyze and rank files by complexity.
+
+#### 3. Understanding Dependencies
+
+```
+You: What does the UserService depend on?
+```
+
+ipuaro will use `get_dependencies` to show imported modules.
+
+```
+You: What files use the validation utilities?
+```
+
+ipuaro will use `get_dependents` to show files importing validation.ts.
+
+#### 4. Code Analysis
+
+```
+You: Find all references to the ValidationError class
+```
+
+ipuaro will use `find_references` to locate all usages.
+
+```
+You: Where is the Logger class defined?
+```
+
+ipuaro will use `find_definition` to locate the definition.
+
+#### 5. Making Changes
+
+```
+You: Add a method to UserService to count total users
+```
+
+ipuaro will:
+1. Read UserService class with `get_class`
+2. Generate the new method
+3. Use `edit_lines` to add it
+4. Show diff and ask for confirmation
+
+```
+You: Fix the TODO in validation.ts about password validation
+```
+
+ipuaro will:
+1. Find the TODO with `get_todos`
+2. Read the function with `get_function`
+3. Implement stronger password validation
+4. Use `edit_lines` to apply changes
+
+#### 6. Testing
+
+```
+You: Run the tests
+```
+
+ipuaro will use `run_tests` to execute the test suite.
+
+```
+You: Add a test for the getUserByEmail method
+```
+
+ipuaro will:
+1. Read existing tests with `get_lines`
+2. Generate new test following the pattern
+3. Use `edit_lines` to add it
+
+#### 7. Git Operations
+
+```
+You: What files have I changed?
+```
+
+ipuaro will use `git_status` to show modified files.
+
+```
+You: Show me the diff for UserService
+```
+
+ipuaro will use `git_diff` with the file path.
+
+```
+You: Commit these changes with message "feat: add user count method"
+```
+
+ipuaro will use `git_commit` after confirmation.
+
+## Tool Demonstration Scenarios
+
+### Scenario 1: Bug Fix Flow
+
+```
+You: There's a bug - we need to sanitize user input before storing. Fix this in UserService.
+
+Agent will:
+1. get_function("src/services/user.ts", "createUser")
+2. See that sanitization is missing
+3. find_definition("sanitizeInput") to locate the utility
+4. edit_lines to add sanitization call
+5. run_tests to verify the fix
+```
+
+### Scenario 2: Refactoring Flow
+
+```
+You: Extract the ID generation logic into a separate utility function
+
+Agent will:
+1. get_class("src/services/user.ts", "UserService")
+2. Find generateId private method
+3. create_file("src/utils/id.ts") with the utility
+4. edit_lines to replace private method with import
+5. find_references("generateId") to check no other usages
+6. run_tests to ensure nothing broke
+```
+
+### Scenario 3: Feature Addition
+
+```
+You: Add password reset functionality to AuthService
+
+Agent will:
+1. get_class("src/auth/service.ts", "AuthService")
+2. get_dependencies to see what's available
+3. Design the resetPassword method
+4. edit_lines to add the method
+5. Suggest creating a test
+6. create_file("tests/auth.test.ts") if needed
+```
+
+### Scenario 4: Code Review
+
+```
+You: Review the code for security issues
+
+Agent will:
+1. get_todos to find FIXME about XSS
+2. get_complexity to find complex functions
+3. get_function for suspicious functions
+4. Suggest improvements
+5. Optionally edit_lines to fix issues
+```
+
+## Slash Commands
+
+While exploring, you can use these commands:
+
+```
+/help               # Show all commands and hotkeys
+/status             # Show system status (LLM, Redis, context)
+/sessions list      # List all sessions
+/undo               # Undo last file change
+/clear              # Clear chat history
+/reindex            # Force project reindexation
+/auto-apply on      # Enable auto-apply mode (skip confirmations)
+```
+
+## Hotkeys
+
+- `Ctrl+C` - Interrupt generation (1st) / Exit (2nd within 1s)
+- `Ctrl+D` - Exit and save session
+- `Ctrl+Z` - Undo last change
+- `↑` / `↓` - Navigate input history
+
+## Project Files Overview
+
+```
+demo-project/
+├── src/
+│   ├── auth/
+│   │   └── service.ts       # Authentication logic (login, logout, verify)
+│   ├── services/
+│   │   └── user.ts          # User CRUD operations
+│   ├── utils/
+│   │   ├── logger.ts        # Logging utility (multiple methods)
+│   │   └── validation.ts    # Input validation (with TODOs/FIXMEs)
+│   ├── types/
+│   │   └── user.ts          # TypeScript type definitions
+│   └── index.ts             # Application entry point
+├── tests/
+│   └── user.test.ts         # User service tests (vitest)
+├── package.json             # Project configuration
+├── tsconfig.json            # TypeScript configuration
+├── vitest.config.ts         # Test configuration
+└── .ipuaro.json             # ipuaro configuration
+```
+
+## What ipuaro Can Do With This Project
+
+### Read Tools ✅
+- **get_lines**: Read any file or specific line ranges
+- **get_function**: Extract specific functions (login, createUser, etc.)
+- **get_class**: Extract classes (UserService, AuthService, Logger, etc.)
+- **get_structure**: See directory tree
+
+### Edit Tools ✅
+- **edit_lines**: Modify functions, fix bugs, add features
+- **create_file**: Add new utilities, tests, services
+- **delete_file**: Remove unused files
+
+### Search Tools ✅
+- **find_references**: Find all usages of ValidationError, User, etc.
+- **find_definition**: Locate where Logger, UserService are defined
+
+### Analysis Tools ✅
+- **get_dependencies**: See what UserService imports
+- **get_dependents**: See what imports validation.ts (multiple files!)
+- **get_complexity**: Identify complex functions (createUser has moderate complexity)
+- **get_todos**: Find 2 TODOs and 1 FIXME in the project
+
+### Git Tools ✅
+- **git_status**: Check working tree
+- **git_diff**: See changes
+- **git_commit**: Commit with AI-generated messages
+
+### Run Tools ✅
+- **run_command**: Execute npm scripts
+- **run_tests**: Run vitest tests
+
+## Tips for Best Experience
+
+1. **Start Small**: Ask about structure first, then dive into specific files
+2. **Be Specific**: "Show me the createUser function" vs "How does this work?"
+3. **Use Tools Implicitly**: Just ask questions, let ipuaro choose the right tools
+4. **Review Changes**: Always review diffs before applying edits
+5. **Test Often**: Ask ipuaro to run tests after making changes
+6. **Commit Incrementally**: Use git_commit for each logical change
+
+## Advanced Workflows
+
+### Workflow 1: Add New Feature
+
+```
+You: Add email verification to the authentication flow
+
+Agent will:
+1. Analyze current auth flow
+2. Propose design (new fields, methods)
+3. Edit AuthService to add verification
+4. Edit User types to add verified field
+5. Create tests for verification
+6. Run tests
+7. Offer to commit
+```
+
+### Workflow 2: Performance Optimization
+
+```
+You: The user lookup is slow when we have many users. Optimize it.
+
+Agent will:
+1. Analyze UserService.getUserByEmail
+2. See it's using Array.find (O(n))
+3. Suggest adding an email index
+4. Edit to add private emailIndex: Map<string, User>
+5. Update createUser to populate index
+6. Update deleteUser to maintain index
+7. Run tests to verify
+```
+
+### Workflow 3: Security Audit
+
+```
+You: Audit the code for security vulnerabilities
+
+Agent will:
+1. get_todos to find FIXME about XSS
+2. Review sanitizeInput implementation
+3. Check password validation strength
+4. Look for SQL injection risks (none here)
+5. Suggest improvements
+6. Optionally implement fixes
+```
+
+## Next Steps
+
+After exploring the demo project, try:
+
+1. **Your Own Project**: Run `ipuaro` in your real codebase
+2. **Customize Config**: Edit `.ipuaro.json` to fit your needs
+3. **Different Model**: Try `--model qwen2.5-coder:32b-instruct` for better results
+4. **Auto-Apply Mode**: Use `--auto-apply` for faster iterations (with caution!)
+
+## Troubleshooting
+
+### Redis Not Connected
+```bash
+# Start Redis with persistence
+redis-server --appendonly yes
+```
+
+### Ollama Model Not Found
+```bash
+# Pull the model
+ollama pull qwen2.5-coder:7b-instruct
+
+# Check it's installed
+ollama list
+```
+
+### Indexing Takes Long
+The project is small (~10 files) so indexing should be instant. For larger projects, use ignore patterns in `.ipuaro.json`.
+
+## Learn More
+
+- [ipuaro Documentation](../../README.md)
+- [Architecture Guide](../../ARCHITECTURE.md)
+- [Tools Reference](../../TOOLS.md)
+- [GitHub Repository](https://github.com/samiyev/puaros)
+
+---
+
+**Happy coding with ipuaro!** 🎩✨

packages/ipuaro/examples/demo-project/package.json

@@ -0,0 +1,20 @@
+{
+    "name": "ipuaro-demo-project",
+    "version": "1.0.0",
+    "description": "Demo project for ipuaro - showcasing AI agent capabilities",
+    "private": true,
+    "type": "module",
+    "scripts": {
+        "dev": "tsx src/index.ts",
+        "test": "vitest",
+        "test:run": "vitest run",
+        "build": "tsc"
+    },
+    "dependencies": {},
+    "devDependencies": {
+        "@types/node": "^22.10.1",
+        "tsx": "^4.19.2",
+        "typescript": "^5.7.2",
+        "vitest": "^1.6.0"
+    }
+}

packages/ipuaro/examples/demo-project/src/auth/service.ts

@@ -0,0 +1,85 @@
+/**
+ * Authentication service
+ */
+
+import type { User, AuthToken } from "../types/user"
+import { UserService } from "../services/user"
+import { createLogger } from "../utils/logger"
+
+const logger = createLogger("AuthService")
+
+export class AuthService {
+    private tokens: Map<string, AuthToken> = new Map()
+
+    constructor(private userService: UserService) {}
+
+    async login(email: string, password: string): Promise<AuthToken> {
+        logger.info("Login attempt", { email })
+
+        // Get user
+        const user = await this.userService.getUserByEmail(email)
+        if (!user) {
+            logger.warn("Login failed - user not found", { email })
+            throw new Error("Invalid credentials")
+        }
+
+        // TODO: Implement actual password verification
+        // For demo purposes, we just check if password is provided
+        if (!password) {
+            logger.warn("Login failed - no password", { email })
+            throw new Error("Invalid credentials")
+        }
+
+        // Generate token
+        const token = this.generateToken(user)
+        this.tokens.set(token.token, token)
+
+        logger.info("Login successful", { userId: user.id })
+        return token
+    }
+
+    async logout(tokenString: string): Promise<void> {
+        logger.info("Logout", { token: tokenString.substring(0, 10) + "..." })
+
+        const token = this.tokens.get(tokenString)
+        if (!token) {
+            throw new Error("Invalid token")
+        }
+
+        this.tokens.delete(tokenString)
+        logger.info("Logout successful", { userId: token.userId })
+    }
+
+    async verifyToken(tokenString: string): Promise<User> {
+        logger.debug("Verifying token")
+
+        const token = this.tokens.get(tokenString)
+        if (!token) {
+            throw new Error("Invalid token")
+        }
+
+        if (token.expiresAt < new Date()) {
+            this.tokens.delete(tokenString)
+            throw new Error("Token expired")
+        }
+
+        const user = await this.userService.getUserById(token.userId)
+        if (!user) {
+            throw new Error("User not found")
+        }
+
+        return user
+    }
+
+    private generateToken(user: User): AuthToken {
+        const token = `tok_${Date.now()}_${Math.random().toString(36).substring(7)}`
+        const expiresAt = new Date()
+        expiresAt.setHours(expiresAt.getHours() + 24) // 24 hours
+
+        return {
+            token,
+            expiresAt,
+            userId: user.id,
+        }
+    }
+}

packages/ipuaro/examples/demo-project/src/index.ts

@@ -0,0 +1,48 @@
+/**
+ * Demo application entry point
+ */
+
+import { UserService } from "./services/user"
+import { AuthService } from "./auth/service"
+import { createLogger } from "./utils/logger"
+
+const logger = createLogger("App")
+
+async function main(): Promise<void> {
+    logger.info("Starting demo application")
+
+    // Initialize services
+    const userService = new UserService()
+    const authService = new AuthService(userService)
+
+    try {
+        // Create a demo user
+        const user = await userService.createUser({
+            email: "demo@example.com",
+            name: "Demo User",
+            password: "password123",
+            role: "admin",
+        })
+
+        logger.info("Demo user created", { userId: user.id })
+
+        // Login
+        const token = await authService.login("demo@example.com", "password123")
+        logger.info("Login successful", { token: token.token })
+
+        // Verify token
+        const verifiedUser = await authService.verifyToken(token.token)
+        logger.info("Token verified", { userId: verifiedUser.id })
+
+        // Logout
+        await authService.logout(token.token)
+        logger.info("Logout successful")
+    } catch (error) {
+        logger.error("Application error", error as Error)
+        process.exit(1)
+    }
+
+    logger.info("Demo application finished")
+}
+
+main()

packages/ipuaro/examples/demo-project/src/services/user.ts

@@ -0,0 +1,100 @@
+/**
+ * User service - handles user-related operations
+ */
+
+import type { User, CreateUserDto, UpdateUserDto } from "../types/user"
+import { isValidEmail, isStrongPassword, ValidationError } from "../utils/validation"
+import { createLogger } from "../utils/logger"
+
+const logger = createLogger("UserService")
+
+export class UserService {
+    private users: Map<string, User> = new Map()
+
+    async createUser(dto: CreateUserDto): Promise<User> {
+        logger.info("Creating user", { email: dto.email })
+
+        // Validate email
+        if (!isValidEmail(dto.email)) {
+            throw new ValidationError("Invalid email address", "email")
+        }
+
+        // Validate password
+        if (!isStrongPassword(dto.password)) {
+            throw new ValidationError("Password must be at least 8 characters", "password")
+        }
+
+        // Check if user already exists
+        const existingUser = Array.from(this.users.values()).find((u) => u.email === dto.email)
+
+        if (existingUser) {
+            throw new Error("User with this email already exists")
+        }
+
+        // Create user
+        const user: User = {
+            id: this.generateId(),
+            email: dto.email,
+            name: dto.name,
+            role: dto.role || "user",
+            createdAt: new Date(),
+            updatedAt: new Date(),
+        }
+
+        this.users.set(user.id, user)
+        logger.info("User created", { userId: user.id })
+
+        return user
+    }
+
+    async getUserById(id: string): Promise<User | null> {
+        logger.debug("Getting user by ID", { userId: id })
+        return this.users.get(id) || null
+    }
+
+    async getUserByEmail(email: string): Promise<User | null> {
+        logger.debug("Getting user by email", { email })
+        return Array.from(this.users.values()).find((u) => u.email === email) || null
+    }
+
+    async updateUser(id: string, dto: UpdateUserDto): Promise<User> {
+        logger.info("Updating user", { userId: id })
+
+        const user = this.users.get(id)
+        if (!user) {
+            throw new Error("User not found")
+        }
+
+        const updated: User = {
+            ...user,
+            ...(dto.name && { name: dto.name }),
+            ...(dto.role && { role: dto.role }),
+            updatedAt: new Date(),
+        }
+
+        this.users.set(id, updated)
+        logger.info("User updated", { userId: id })
+
+        return updated
+    }
+
+    async deleteUser(id: string): Promise<void> {
+        logger.info("Deleting user", { userId: id })
+
+        if (!this.users.has(id)) {
+            throw new Error("User not found")
+        }
+
+        this.users.delete(id)
+        logger.info("User deleted", { userId: id })
+    }
+
+    async listUsers(): Promise<User[]> {
+        logger.debug("Listing all users")
+        return Array.from(this.users.values())
+    }
+
+    private generateId(): string {
+        return `user_${Date.now()}_${Math.random().toString(36).substring(7)}`
+    }
+}

packages/ipuaro/examples/demo-project/src/types/user.ts

@@ -0,0 +1,32 @@
+/**
+ * User-related type definitions
+ */
+
+export interface User {
+    id: string
+    email: string
+    name: string
+    role: UserRole
+    createdAt: Date
+    updatedAt: Date
+}
+
+export type UserRole = "admin" | "user" | "guest"
+
+export interface CreateUserDto {
+    email: string
+    name: string
+    password: string
+    role?: UserRole
+}
+
+export interface UpdateUserDto {
+    name?: string
+    role?: UserRole
+}
+
+export interface AuthToken {
+    token: string
+    expiresAt: Date
+    userId: string
+}

packages/ipuaro/examples/demo-project/src/utils/logger.ts

@@ -0,0 +1,41 @@
+/**
+ * Simple logging utility
+ */
+
+export type LogLevel = "debug" | "info" | "warn" | "error"
+
+export class Logger {
+    constructor(private context: string) {}
+
+    debug(message: string, meta?: Record<string, unknown>): void {
+        this.log("debug", message, meta)
+    }
+
+    info(message: string, meta?: Record<string, unknown>): void {
+        this.log("info", message, meta)
+    }
+
+    warn(message: string, meta?: Record<string, unknown>): void {
+        this.log("warn", message, meta)
+    }
+
+    error(message: string, error?: Error, meta?: Record<string, unknown>): void {
+        this.log("error", message, { ...meta, error: error?.message })
+    }
+
+    private log(level: LogLevel, message: string, meta?: Record<string, unknown>): void {
+        const timestamp = new Date().toISOString()
+        const logEntry = {
+            timestamp,
+            level,
+            context: this.context,
+            message,
+            ...(meta && { meta }),
+        }
+        console.log(JSON.stringify(logEntry))
+    }
+}
+
+export function createLogger(context: string): Logger {
+    return new Logger(context)
+}

packages/ipuaro/examples/demo-project/src/utils/validation.ts

@@ -0,0 +1,28 @@
+/**
+ * Validation utilities
+ */
+
+export function isValidEmail(email: string): boolean {
+    const emailRegex = /^[^\s@]+@[^\s@]+\.[^\s@]+$/
+    return emailRegex.test(email)
+}
+
+export function isStrongPassword(password: string): boolean {
+    // TODO: Add more sophisticated password validation
+    return password.length >= 8
+}
+
+export function sanitizeInput(input: string): string {
+    // FIXME: This is a basic implementation, needs XSS protection
+    return input.trim().replace(/[<>]/g, "")
+}
+
+export class ValidationError extends Error {
+    constructor(
+        message: string,
+        public field: string,
+    ) {
+        super(message)
+        this.name = "ValidationError"
+    }
+}

packages/ipuaro/examples/demo-project/tests/user.test.ts

@@ -0,0 +1,141 @@
+/**
+ * User service tests
+ */
+
+import { describe, it, expect, beforeEach } from "vitest"
+import { UserService } from "../src/services/user"
+import { ValidationError } from "../src/utils/validation"
+
+describe("UserService", () => {
+    let userService: UserService
+
+    beforeEach(() => {
+        userService = new UserService()
+    })
+
+    describe("createUser", () => {
+        it("should create a new user", async () => {
+            const user = await userService.createUser({
+                email: "test@example.com",
+                name: "Test User",
+                password: "password123",
+            })
+
+            expect(user).toBeDefined()
+            expect(user.email).toBe("test@example.com")
+            expect(user.name).toBe("Test User")
+            expect(user.role).toBe("user")
+        })
+
+        it("should reject invalid email", async () => {
+            await expect(
+                userService.createUser({
+                    email: "invalid-email",
+                    name: "Test User",
+                    password: "password123",
+                }),
+            ).rejects.toThrow(ValidationError)
+        })
+
+        it("should reject weak password", async () => {
+            await expect(
+                userService.createUser({
+                    email: "test@example.com",
+                    name: "Test User",
+                    password: "weak",
+                }),
+            ).rejects.toThrow(ValidationError)
+        })
+
+        it("should prevent duplicate emails", async () => {
+            await userService.createUser({
+                email: "test@example.com",
+                name: "Test User",
+                password: "password123",
+            })
+
+            await expect(
+                userService.createUser({
+                    email: "test@example.com",
+                    name: "Another User",
+                    password: "password123",
+                }),
+            ).rejects.toThrow("already exists")
+        })
+    })
+
+    describe("getUserById", () => {
+        it("should return user by ID", async () => {
+            const created = await userService.createUser({
+                email: "test@example.com",
+                name: "Test User",
+                password: "password123",
+            })
+
+            const found = await userService.getUserById(created.id)
+            expect(found).toEqual(created)
+        })
+
+        it("should return null for non-existent ID", async () => {
+            const found = await userService.getUserById("non-existent")
+            expect(found).toBeNull()
+        })
+    })
+
+    describe("updateUser", () => {
+        it("should update user name", async () => {
+            const user = await userService.createUser({
+                email: "test@example.com",
+                name: "Test User",
+                password: "password123",
+            })
+
+            const updated = await userService.updateUser(user.id, {
+                name: "Updated Name",
+            })
+
+            expect(updated.name).toBe("Updated Name")
+            expect(updated.email).toBe(user.email)
+        })
+
+        it("should throw error for non-existent user", async () => {
+            await expect(userService.updateUser("non-existent", { name: "Test" })).rejects.toThrow(
+                "not found",
+            )
+        })
+    })
+
+    describe("deleteUser", () => {
+        it("should delete user", async () => {
+            const user = await userService.createUser({
+                email: "test@example.com",
+                name: "Test User",
+                password: "password123",
+            })
+
+            await userService.deleteUser(user.id)
+
+            const found = await userService.getUserById(user.id)
+            expect(found).toBeNull()
+        })
+    })
+
+    describe("listUsers", () => {
+        it("should return all users", async () => {
+            await userService.createUser({
+                email: "user1@example.com",
+                name: "User 1",
+                password: "password123",
+            })
+
+            await userService.createUser({
+                email: "user2@example.com",
+                name: "User 2",
+                password: "password123",
+            })
+
+            const users = await userService.listUsers()
+            expect(users).toHaveLength(2)
+        })
+    })
+})

packages/ipuaro/examples/demo-project/tsconfig.json

@@ -0,0 +1,16 @@
+{
+    "compilerOptions": {
+        "target": "ES2023",
+        "module": "ESNext",
+        "lib": ["ES2023"],
+        "moduleResolution": "Bundler",
+        "esModuleInterop": true,
+        "strict": true,
+        "skipLibCheck": true,
+        "resolveJsonModule": true,
+        "outDir": "dist",
+        "rootDir": "src"
+    },
+    "include": ["src/**/*"],
+    "exclude": ["node_modules", "dist", "tests"]
+}

packages/ipuaro/examples/demo-project/vitest.config.ts

@@ -0,0 +1,8 @@
+import { defineConfig } from "vitest/config"
+
+export default defineConfig({
+    test: {
+        globals: true,
+        environment: "node",
+    },
+})

packages/ipuaro/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@samiyev/ipuaro",
-    "version": "0.12.0",
+    "version": "0.30.1",
     "description": "Local AI agent for codebase operations with infinite context feeling",
     "author": "Fozilbek Samiyev <fozilbek.samiyev@gmail.com>",
     "license": "MIT",
@@ -8,7 +8,7 @@
     "main": "./dist/index.js",
     "types": "./dist/index.d.ts",
     "bin": {
-        "ipuaro": "./bin/ipuaro.js"
+        "ipuaro": "bin/ipuaro.js"
     },
     "exports": {
         ".": {
@@ -44,14 +44,20 @@
         "simple-git": "^3.27.0",
         "tree-sitter": "^0.21.1",
         "tree-sitter-javascript": "^0.21.0",
+        "tree-sitter-json": "^0.24.8",
         "tree-sitter-typescript": "^0.21.2",
+        "yaml": "^2.8.2",
         "zod": "^3.23.8"
     },
     "devDependencies": {
+        "@testing-library/react": "^16.3.0",
+        "@types/jsdom": "^27.0.0",
         "@types/node": "^22.10.1",
         "@types/react": "^18.2.0",
         "@vitest/coverage-v8": "^1.6.0",
         "@vitest/ui": "^1.6.0",
+        "jsdom": "^27.2.0",
+        "react-dom": "18.3.1",
         "tsup": "^8.3.5",
         "typescript": "^5.7.2",
         "vitest": "^1.6.0"

packages/ipuaro/src/application/use-cases/ContextManager.ts

@@ -2,6 +2,7 @@ import type { ContextState, Session } from "../../domain/entities/Session.js"
 import type { ILLMClient } from "../../domain/services/ILLMClient.js"
 import { type ChatMessage, createSystemMessage } from "../../domain/value-objects/ChatMessage.js"
 import { CONTEXT_COMPRESSION_THRESHOLD, CONTEXT_WINDOW_SIZE } from "../../domain/constants/index.js"
+import type { ContextConfig } from "../../shared/constants/config.js"
 
 /**
  * File in context with token count.
@@ -39,9 +40,13 @@ export class ContextManager {
     private readonly filesInContext = new Map<string, FileContext>()
     private currentTokens = 0
     private readonly contextWindowSize: number
+    private readonly compressionThreshold: number
+    private readonly compressionMethod: "llm-summary" | "truncate"
 
-    constructor(contextWindowSize: number = CONTEXT_WINDOW_SIZE) {
+    constructor(contextWindowSize: number = CONTEXT_WINDOW_SIZE, config?: ContextConfig) {
         this.contextWindowSize = contextWindowSize
+        this.compressionThreshold = config?.autoCompressAt ?? CONTEXT_COMPRESSION_THRESHOLD
+        this.compressionMethod = config?.compressionMethod ?? "llm-summary"
     }
 
     /**
@@ -97,7 +102,7 @@ export class ContextManager {
      * Check if compression is needed.
      */
     needsCompression(): boolean {
-        return this.getUsage() > CONTEXT_COMPRESSION_THRESHOLD
+        return this.getUsage() > this.compressionThreshold
     }
 
     /**

packages/ipuaro/src/application/use-cases/ExecuteTool.ts

@@ -0,0 +1,224 @@
+import { randomUUID } from "node:crypto"
+import type { Session } from "../../domain/entities/Session.js"
+import type { ISessionStorage } from "../../domain/services/ISessionStorage.js"
+import type { IStorage } from "../../domain/services/IStorage.js"
+import type { DiffInfo, ToolContext } from "../../domain/services/ITool.js"
+import type { ToolCall } from "../../domain/value-objects/ToolCall.js"
+import { createErrorResult, type ToolResult } from "../../domain/value-objects/ToolResult.js"
+import { createUndoEntry } from "../../domain/value-objects/UndoEntry.js"
+import type { IToolRegistry } from "../interfaces/IToolRegistry.js"
+
+/**
+ * Result of confirmation dialog.
+ */
+export interface ConfirmationResult {
+    confirmed: boolean
+    editedContent?: string[]
+}
+
+/**
+ * Confirmation handler callback type.
+ * Can return either a boolean (for backward compatibility) or a ConfirmationResult.
+ */
+export type ConfirmationHandler = (
+    message: string,
+    diff?: DiffInfo,
+) => Promise<boolean | ConfirmationResult>
+
+/**
+ * Progress handler callback type.
+ */
+export type ProgressHandler = (message: string) => void
+
+/**
+ * Options for ExecuteTool.
+ */
+export interface ExecuteToolOptions {
+    /** Auto-apply edits without confirmation */
+    autoApply?: boolean
+    /** Confirmation handler */
+    onConfirmation?: ConfirmationHandler
+    /** Progress handler */
+    onProgress?: ProgressHandler
+}
+
+/**
+ * Result of tool execution.
+ */
+export interface ExecuteToolResult {
+    result: ToolResult
+    undoEntryCreated: boolean
+    undoEntryId?: string
+}
+
+/**
+ * Use case for executing a single tool.
+ * Orchestrates tool execution with:
+ * - Parameter validation
+ * - Confirmation flow
+ * - Undo stack management
+ * - Storage updates
+ */
+export class ExecuteTool {
+    private readonly storage: IStorage
+    private readonly sessionStorage: ISessionStorage
+    private readonly tools: IToolRegistry
+    private readonly projectRoot: string
+    private lastUndoEntryId?: string
+
+    constructor(
+        storage: IStorage,
+        sessionStorage: ISessionStorage,
+        tools: IToolRegistry,
+        projectRoot: string,
+    ) {
+        this.storage = storage
+        this.sessionStorage = sessionStorage
+        this.tools = tools
+        this.projectRoot = projectRoot
+    }
+
+    /**
+     * Execute a tool call.
+     *
+     * @param toolCall - The tool call to execute
+     * @param session - Current session (for undo stack)
+     * @param options - Execution options
+     * @returns Execution result
+     */
+    async execute(
+        toolCall: ToolCall,
+        session: Session,
+        options: ExecuteToolOptions = {},
+    ): Promise<ExecuteToolResult> {
+        this.lastUndoEntryId = undefined
+        const startTime = Date.now()
+        const tool = this.tools.get(toolCall.name)
+
+        if (!tool) {
+            return {
+                result: createErrorResult(
+                    toolCall.id,
+                    `Unknown tool: ${toolCall.name}`,
+                    Date.now() - startTime,
+                ),
+                undoEntryCreated: false,
+            }
+        }
+
+        const validationError = tool.validateParams(toolCall.params)
+        if (validationError) {
+            return {
+                result: createErrorResult(toolCall.id, validationError, Date.now() - startTime),
+                undoEntryCreated: false,
+            }
+        }
+
+        const context = this.buildToolContext(toolCall, session, options)
+
+        try {
+            const result = await tool.execute(toolCall.params, context)
+
+            return {
+                result,
+                undoEntryCreated: this.lastUndoEntryId !== undefined,
+                undoEntryId: this.lastUndoEntryId,
+            }
+        } catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error)
+            return {
+                result: createErrorResult(toolCall.id, errorMessage, Date.now() - startTime),
+                undoEntryCreated: false,
+            }
+        }
+    }
+
+    /**
+     * Build tool context for execution.
+     */
+    private buildToolContext(
+        toolCall: ToolCall,
+        session: Session,
+        options: ExecuteToolOptions,
+    ): ToolContext {
+        return {
+            projectRoot: this.projectRoot,
+            storage: this.storage,
+            requestConfirmation: async (msg: string, diff?: DiffInfo) => {
+                return this.handleConfirmation(msg, diff, toolCall, session, options)
+            },
+            onProgress: (msg: string) => {
+                options.onProgress?.(msg)
+            },
+        }
+    }
+
+    /**
+     * Handle confirmation for tool actions.
+     * Supports edited content from user.
+     */
+    private async handleConfirmation(
+        msg: string,
+        diff: DiffInfo | undefined,
+        toolCall: ToolCall,
+        session: Session,
+        options: ExecuteToolOptions,
+    ): Promise<boolean> {
+        if (options.autoApply) {
+            if (diff) {
+                this.lastUndoEntryId = await this.createUndoEntry(diff, toolCall, session)
+            }
+            return true
+        }
+
+        if (options.onConfirmation) {
+            const result = await options.onConfirmation(msg, diff)
+
+            const confirmed = typeof result === "boolean" ? result : result.confirmed
+            const editedContent = typeof result === "boolean" ? undefined : result.editedContent
+
+            if (confirmed && diff) {
+                if (editedContent && editedContent.length > 0) {
+                    diff.newLines = editedContent
+                    if (toolCall.params.content && typeof toolCall.params.content === "string") {
+                        toolCall.params.content = editedContent.join("\n")
+                    }
+                }
+
+                this.lastUndoEntryId = await this.createUndoEntry(diff, toolCall, session)
+            }
+
+            return confirmed
+        }
+
+        if (diff) {
+            this.lastUndoEntryId = await this.createUndoEntry(diff, toolCall, session)
+        }
+        return true
+    }
+
+    /**
+     * Create undo entry from diff.
+     */
+    private async createUndoEntry(
+        diff: DiffInfo,
+        toolCall: ToolCall,
+        session: Session,
+    ): Promise<string> {
+        const entryId = randomUUID()
+        const entry = createUndoEntry(
+            entryId,
+            diff.filePath,
+            diff.oldLines,
+            diff.newLines,
+            `${toolCall.name}: ${diff.filePath}`,
+            toolCall.id,
+        )
+
+        session.addUndoEntry(entry)
+        await this.sessionStorage.pushUndoEntry(session.id, entry)
+        session.stats.editsApplied++
+
+        return entryId
+    }
+}

packages/ipuaro/src/application/use-cases/HandleMessage.ts

@@ -1,9 +1,8 @@
-import { randomUUID } from "node:crypto"
 import type { Session } from "../../domain/entities/Session.js"
 import type { ILLMClient } from "../../domain/services/ILLMClient.js"
 import type { ISessionStorage } from "../../domain/services/ISessionStorage.js"
 import type { IStorage } from "../../domain/services/IStorage.js"
-import type { DiffInfo, ToolContext } from "../../domain/services/ITool.js"
+import type { DiffInfo } from "../../domain/services/ITool.js"
 import {
     type ChatMessage,
     createAssistantMessage,
@@ -12,18 +11,19 @@ import {
     createUserMessage,
 } from "../../domain/value-objects/ChatMessage.js"
 import type { ToolCall } from "../../domain/value-objects/ToolCall.js"
-import { createErrorResult, type ToolResult } from "../../domain/value-objects/ToolResult.js"
-import { createUndoEntry, type UndoEntry } from "../../domain/value-objects/UndoEntry.js"
-import { IpuaroError } from "../../shared/errors/IpuaroError.js"
-import type { ErrorChoice } from "../../shared/types/index.js"
+import type { ToolResult } from "../../domain/value-objects/ToolResult.js"
+import type { UndoEntry } from "../../domain/value-objects/UndoEntry.js"
+import { type ErrorOption, IpuaroError } from "../../shared/errors/IpuaroError.js"
 import {
     buildInitialContext,
     type ProjectStructure,
     SYSTEM_PROMPT,
+    TOOL_REMINDER,
 } from "../../infrastructure/llm/prompts.js"
 import { parseToolCalls } from "../../infrastructure/llm/ResponseParser.js"
 import type { IToolRegistry } from "../interfaces/IToolRegistry.js"
 import { ContextManager } from "./ContextManager.js"
+import { type ConfirmationResult, ExecuteTool } from "./ExecuteTool.js"
 
 /**
  * Status during message handling.
@@ -57,8 +57,8 @@ export interface HandleMessageEvents {
     onMessage?: (message: ChatMessage) => void
     onToolCall?: (call: ToolCall) => void
     onToolResult?: (result: ToolResult) => void
-    onConfirmation?: (message: string, diff?: DiffInfo) => Promise<boolean>
-    onError?: (error: IpuaroError) => Promise<ErrorChoice>
+    onConfirmation?: (message: string, diff?: DiffInfo) => Promise<boolean | ConfirmationResult>
+    onError?: (error: IpuaroError) => Promise<ErrorOption>
     onStatusChange?: (status: HandleMessageStatus) => void
     onUndoEntry?: (entry: UndoEntry) => void
 }
@@ -69,6 +69,9 @@ export interface HandleMessageEvents {
 export interface HandleMessageOptions {
     autoApply?: boolean
     maxToolCalls?: number
+    maxHistoryMessages?: number
+    saveInputHistory?: boolean
+    contextConfig?: import("../../shared/constants/config.js").ContextConfig
 }
 
 const DEFAULT_MAX_TOOL_CALLS = 20
@@ -83,6 +86,7 @@ export class HandleMessage {
     private readonly llm: ILLMClient
     private readonly tools: IToolRegistry
     private readonly contextManager: ContextManager
+    private readonly executeTool: ExecuteTool
     private readonly projectRoot: string
     private projectStructure?: ProjectStructure
 
@@ -96,13 +100,15 @@ export class HandleMessage {
         llm: ILLMClient,
         tools: IToolRegistry,
         projectRoot: string,
+        contextConfig?: import("../../shared/constants/config.js").ContextConfig,
     ) {
         this.storage = storage
         this.sessionStorage = sessionStorage
         this.llm = llm
         this.tools = tools
         this.projectRoot = projectRoot
-        this.contextManager = new ContextManager(llm.getContextWindowSize())
+        this.contextManager = new ContextManager(llm.getContextWindowSize(), contextConfig)
+        this.executeTool = new ExecuteTool(storage, sessionStorage, tools, projectRoot)
     }
 
     /**
@@ -134,6 +140,15 @@ export class HandleMessage {
         this.llm.abort()
     }
 
+    /**
+     * Truncate session history if maxHistoryMessages is set.
+     */
+    private truncateHistoryIfNeeded(session: Session): void {
+        if (this.options.maxHistoryMessages !== undefined) {
+            session.truncateHistory(this.options.maxHistoryMessages)
+        }
+    }
+
     /**
      * Execute the message handling flow.
      */
@@ -144,7 +159,12 @@ export class HandleMessage {
         if (message.trim()) {
             const userMessage = createUserMessage(message)
             session.addMessage(userMessage)
-            session.addInputToHistory(message)
+            this.truncateHistoryIfNeeded(session)
+
+            if (this.options.saveInputHistory !== false) {
+                session.addInputToHistory(message)
+            }
+
             this.emitMessage(userMessage)
         }
 
@@ -182,6 +202,7 @@ export class HandleMessage {
                     toolCalls: 0,
                 })
                 session.addMessage(assistantMessage)
+                this.truncateHistoryIfNeeded(session)
                 this.emitMessage(assistantMessage)
                 this.contextManager.addTokens(response.tokens)
                 this.contextManager.updateSession(session)
@@ -196,6 +217,7 @@ export class HandleMessage {
                 toolCalls: parsed.toolCalls.length,
             })
             session.addMessage(assistantMessage)
+            this.truncateHistoryIfNeeded(session)
             this.emitMessage(assistantMessage)
 
             toolCallCount += parsed.toolCalls.length
@@ -203,6 +225,7 @@ export class HandleMessage {
                 const errorMsg = `Maximum tool calls (${String(maxToolCalls)}) exceeded`
                 const errorMessage = createSystemMessage(errorMsg)
                 session.addMessage(errorMessage)
+                this.truncateHistoryIfNeeded(session)
                 this.emitMessage(errorMessage)
                 this.emitStatus("ready")
                 return
@@ -226,6 +249,7 @@ export class HandleMessage {
 
             const toolMessage = createToolMessage(results)
             session.addMessage(toolMessage)
+            this.truncateHistoryIfNeeded(session)
 
             this.contextManager.addTokens(response.tokens)
 
@@ -254,91 +278,42 @@ export class HandleMessage {
 
         messages.push(...session.history)
 
+        // Add tool reminder if last message is from user (first LLM call for this query)
+        const lastMessage = session.history[session.history.length - 1]
+        if (lastMessage?.role === "user") {
+            messages.push(createSystemMessage(TOOL_REMINDER))
+        }
+
         return messages
     }
 
     private async executeToolCall(toolCall: ToolCall, session: Session): Promise<ToolResult> {
-        const startTime = Date.now()
-        const tool = this.tools.get(toolCall.name)
-
-        if (!tool) {
-            return createErrorResult(
-                toolCall.id,
-                `Unknown tool: ${toolCall.name}`,
-                Date.now() - startTime,
-            )
-        }
-
-        const context: ToolContext = {
-            projectRoot: this.projectRoot,
-            storage: this.storage,
-            requestConfirmation: async (msg: string, diff?: DiffInfo) => {
-                return this.handleConfirmation(msg, diff, toolCall, session)
+        const { result, undoEntryCreated, undoEntryId } = await this.executeTool.execute(
+            toolCall,
+            session,
+            {
+                autoApply: this.options.autoApply,
+                onConfirmation: async (msg: string, diff?: DiffInfo) => {
+                    this.emitStatus("awaiting_confirmation")
+                    if (this.events.onConfirmation) {
+                        return this.events.onConfirmation(msg, diff)
+                    }
+                    return true
+                },
+                onProgress: (_msg: string) => {
+                    this.events.onStatusChange?.("tool_call")
+                },
             },
-            onProgress: (_msg: string) => {
-                this.events.onStatusChange?.("tool_call")
-            },
-        }
-
-        try {
-            const validationError = tool.validateParams(toolCall.params)
-            if (validationError) {
-                return createErrorResult(toolCall.id, validationError, Date.now() - startTime)
-            }
-
-            const result = await tool.execute(toolCall.params, context)
-            return result
-        } catch (error) {
-            const errorMessage = error instanceof Error ? error.message : String(error)
-            return createErrorResult(toolCall.id, errorMessage, Date.now() - startTime)
-        }
-    }
-
-    private async handleConfirmation(
-        msg: string,
-        diff: DiffInfo | undefined,
-        toolCall: ToolCall,
-        session: Session,
-    ): Promise<boolean> {
-        if (this.options.autoApply) {
-            if (diff) {
-                this.createUndoEntryFromDiff(diff, toolCall, session)
-            }
-            return true
-        }
-
-        this.emitStatus("awaiting_confirmation")
-
-        if (this.events.onConfirmation) {
-            const confirmed = await this.events.onConfirmation(msg, diff)
-
-            if (confirmed && diff) {
-                this.createUndoEntryFromDiff(diff, toolCall, session)
-            }
-
-            return confirmed
-        }
-
-        if (diff) {
-            this.createUndoEntryFromDiff(diff, toolCall, session)
-        }
-        return true
-    }
-
-    private createUndoEntryFromDiff(diff: DiffInfo, toolCall: ToolCall, session: Session): void {
-        const entry = createUndoEntry(
-            randomUUID(),
-            diff.filePath,
-            diff.oldLines,
-            diff.newLines,
-            `${toolCall.name}: ${diff.filePath}`,
-            toolCall.id,
         )
 
-        session.addUndoEntry(entry)
-        void this.sessionStorage.pushUndoEntry(session.id, entry)
-        session.stats.editsApplied++
-        this.events.onUndoEntry?.(entry)
+        if (undoEntryCreated && undoEntryId) {
+            const undoEntry = session.undoStack.find((entry) => entry.id === undoEntryId)
+            if (undoEntry) {
+                this.events.onUndoEntry?.(undoEntry)
+            }
+        }
+
+        return result
     }
 
     private async handleLLMError(error: unknown, session: Session): Promise<void> {
@@ -360,6 +335,7 @@ export class HandleMessage {
 
         const errorMessage = createSystemMessage(`Error: ${ipuaroError.message}`)
         session.addMessage(errorMessage)
+        this.truncateHistoryIfNeeded(session)
         this.emitMessage(errorMessage)
 
         this.emitStatus("ready")

packages/ipuaro/src/application/use-cases/IndexProject.ts

@@ -0,0 +1,184 @@
+import * as path from "node:path"
+import type { IStorage } from "../../domain/services/IStorage.js"
+import type { IndexingStats, IndexProgress } from "../../domain/services/IIndexer.js"
+import { FileScanner } from "../../infrastructure/indexer/FileScanner.js"
+import { ASTParser } from "../../infrastructure/indexer/ASTParser.js"
+import { MetaAnalyzer } from "../../infrastructure/indexer/MetaAnalyzer.js"
+import { IndexBuilder } from "../../infrastructure/indexer/IndexBuilder.js"
+import { createFileData, type FileData } from "../../domain/value-objects/FileData.js"
+import type { FileAST } from "../../domain/value-objects/FileAST.js"
+import { md5 } from "../../shared/utils/hash.js"
+
+/**
+ * Options for indexing a project.
+ */
+export interface IndexProjectOptions {
+    /** Additional ignore patterns */
+    additionalIgnore?: string[]
+    /** Progress callback */
+    onProgress?: (progress: IndexProgress) => void
+}
+
+/**
+ * Use case for indexing a project.
+ * Orchestrates the full indexing pipeline:
+ * 1. Scan files
+ * 2. Parse AST
+ * 3. Analyze metadata
+ * 4. Build indexes
+ * 5. Store in Redis
+ */
+export class IndexProject {
+    private readonly storage: IStorage
+    private readonly scanner: FileScanner
+    private readonly parser: ASTParser
+    private readonly metaAnalyzer: MetaAnalyzer
+    private readonly indexBuilder: IndexBuilder
+
+    constructor(storage: IStorage, projectRoot: string) {
+        this.storage = storage
+        this.scanner = new FileScanner()
+        this.parser = new ASTParser()
+        this.metaAnalyzer = new MetaAnalyzer(projectRoot)
+        this.indexBuilder = new IndexBuilder(projectRoot)
+    }
+
+    /**
+     * Execute the indexing pipeline.
+     *
+     * @param projectRoot - Absolute path to project root
+     * @param options - Optional configuration
+     * @returns Indexing statistics
+     */
+    async execute(projectRoot: string, options: IndexProjectOptions = {}): Promise<IndexingStats> {
+        const startTime = Date.now()
+        const stats: IndexingStats = {
+            filesScanned: 0,
+            filesParsed: 0,
+            parseErrors: 0,
+            timeMs: 0,
+        }
+
+        const fileDataMap = new Map<string, FileData>()
+        const astMap = new Map<string, FileAST>()
+        const contentMap = new Map<string, string>()
+
+        // Phase 1: Scanning
+        this.reportProgress(options.onProgress, 0, 0, "", "scanning")
+
+        const scanResults = await this.scanner.scanAll(projectRoot)
+        stats.filesScanned = scanResults.length
+
+        // Phase 2: Parsing
+        let current = 0
+        const total = scanResults.length
+
+        for (const scanResult of scanResults) {
+            current++
+            const fullPath = path.join(projectRoot, scanResult.path)
+            this.reportProgress(options.onProgress, current, total, scanResult.path, "parsing")
+
+            const content = await FileScanner.readFileContent(fullPath)
+            if (!content) {
+                continue
+            }
+
+            contentMap.set(scanResult.path, content)
+
+            const lines = content.split("\n")
+            const hash = md5(content)
+
+            const fileData = createFileData(lines, hash, scanResult.size, scanResult.lastModified)
+            fileDataMap.set(scanResult.path, fileData)
+
+            const language = this.detectLanguage(scanResult.path)
+            if (!language) {
+                continue
+            }
+
+            const ast = this.parser.parse(content, language)
+            astMap.set(scanResult.path, ast)
+
+            stats.filesParsed++
+            if (ast.parseError) {
+                stats.parseErrors++
+            }
+        }
+
+        // Phase 3: Analyzing metadata
+        current = 0
+        for (const [filePath, ast] of astMap) {
+            current++
+            this.reportProgress(options.onProgress, current, astMap.size, filePath, "analyzing")
+
+            const content = contentMap.get(filePath)
+            if (!content) {
+                continue
+            }
+
+            const fullPath = path.join(projectRoot, filePath)
+            const meta = this.metaAnalyzer.analyze(fullPath, ast, content, astMap)
+
+            await this.storage.setMeta(filePath, meta)
+        }
+
+        // Phase 4: Building indexes
+        this.reportProgress(options.onProgress, 1, 1, "Building indexes", "indexing")
+
+        const symbolIndex = this.indexBuilder.buildSymbolIndex(astMap)
+        const depsGraph = this.indexBuilder.buildDepsGraph(astMap)
+
+        // Phase 5: Store everything
+        for (const [filePath, fileData] of fileDataMap) {
+            await this.storage.setFile(filePath, fileData)
+        }
+
+        for (const [filePath, ast] of astMap) {
+            await this.storage.setAST(filePath, ast)
+        }
+
+        await this.storage.setSymbolIndex(symbolIndex)
+        await this.storage.setDepsGraph(depsGraph)
+
+        // Store last indexed timestamp
+        await this.storage.setProjectConfig("last_indexed", Date.now())
+
+        stats.timeMs = Date.now() - startTime
+
+        return stats
+    }
+
+    /**
+     * Detect language from file extension.
+     */
+    private detectLanguage(filePath: string): "ts" | "tsx" | "js" | "jsx" | null {
+        const ext = path.extname(filePath).toLowerCase()
+        switch (ext) {
+            case ".ts":
+                return "ts"
+            case ".tsx":
+                return "tsx"
+            case ".js":
+                return "js"
+            case ".jsx":
+                return "jsx"
+            default:
+                return null
+        }
+    }
+
+    /**
+     * Report progress to callback if provided.
+     */
+    private reportProgress(
+        callback: ((progress: IndexProgress) => void) | undefined,
+        current: number,
+        total: number,
+        currentFile: string,
+        phase: IndexProgress["phase"],
+    ): void {
+        if (callback) {
+            callback({ current, total, currentFile, phase })
+        }
+    }
+}

packages/ipuaro/src/application/use-cases/index.ts

@@ -4,3 +4,5 @@ export * from "./StartSession.js"
 export * from "./HandleMessage.js"
 export * from "./UndoChange.js"
 export * from "./ContextManager.js"
+export * from "./IndexProject.js"
+export * from "./ExecuteTool.js"

packages/ipuaro/src/cli/commands/index-cmd.ts

@@ -0,0 +1,148 @@
+/**
+ * Index command implementation.
+ * Indexes project without starting TUI.
+ */
+
+import * as path from "node:path"
+import { RedisClient } from "../../infrastructure/storage/RedisClient.js"
+import { RedisStorage } from "../../infrastructure/storage/RedisStorage.js"
+import { generateProjectName } from "../../infrastructure/storage/schema.js"
+import { IndexProject } from "../../application/use-cases/IndexProject.js"
+import { type Config, DEFAULT_CONFIG } from "../../shared/constants/config.js"
+import { checkRedis } from "./onboarding.js"
+
+/**
+ * Result of index command.
+ */
+export interface IndexResult {
+    success: boolean
+    filesIndexed: number
+    filesSkipped: number
+    errors: string[]
+    duration: number
+}
+
+/**
+ * Progress callback for indexing.
+ */
+export type IndexProgressCallback = (
+    phase: "scanning" | "parsing" | "analyzing" | "storing",
+    current: number,
+    total: number,
+    currentFile?: string,
+) => void
+
+/**
+ * Execute the index command.
+ */
+export async function executeIndex(
+    projectPath: string,
+    config: Config = DEFAULT_CONFIG,
+    onProgress?: IndexProgressCallback,
+): Promise<IndexResult> {
+    const startTime = Date.now()
+    const resolvedPath = path.resolve(projectPath)
+    const projectName = generateProjectName(resolvedPath)
+
+    console.warn(`📁 Indexing project: ${resolvedPath}`)
+    console.warn(`   Project name: ${projectName}\n`)
+
+    const redisResult = await checkRedis(config.redis)
+    if (!redisResult.ok) {
+        console.error(`❌ ${redisResult.error ?? "Redis unavailable"}`)
+        return {
+            success: false,
+            filesIndexed: 0,
+            filesSkipped: 0,
+            errors: [redisResult.error ?? "Redis unavailable"],
+            duration: Date.now() - startTime,
+        }
+    }
+
+    let redisClient: RedisClient | null = null
+
+    try {
+        redisClient = new RedisClient(config.redis)
+        await redisClient.connect()
+
+        const storage = new RedisStorage(redisClient, projectName)
+        const indexProject = new IndexProject(storage, resolvedPath)
+
+        let lastPhase: "scanning" | "parsing" | "analyzing" | "indexing" = "scanning"
+        let lastProgress = 0
+
+        const stats = await indexProject.execute(resolvedPath, {
+            onProgress: (progress) => {
+                if (progress.phase !== lastPhase) {
+                    if (lastPhase === "scanning") {
+                        console.warn(`   Found ${String(progress.total)} files\n`)
+                    } else if (lastProgress > 0) {
+                        console.warn("")
+                    }
+
+                    const phaseLabels = {
+                        scanning: "🔍 Scanning files...",
+                        parsing: "📝 Parsing files...",
+                        analyzing: "📊 Analyzing metadata...",
+                        indexing: "🏗️  Building indexes...",
+                    }
+                    console.warn(phaseLabels[progress.phase])
+                    lastPhase = progress.phase
+                }
+
+                if (progress.phase === "indexing") {
+                    onProgress?.("storing", progress.current, progress.total)
+                } else {
+                    onProgress?.(
+                        progress.phase,
+                        progress.current,
+                        progress.total,
+                        progress.currentFile,
+                    )
+                }
+
+                if (
+                    progress.current % 50 === 0 &&
+                    progress.phase !== "scanning" &&
+                    progress.phase !== "indexing"
+                ) {
+                    process.stdout.write(
+                        `\r   ${progress.phase === "parsing" ? "Parsed" : "Analyzed"} ${String(progress.current)}/${String(progress.total)} files...`,
+                    )
+                }
+                lastProgress = progress.current
+            },
+        })
+
+        const symbolIndex = await storage.getSymbolIndex()
+        const durationSec = (stats.timeMs / 1000).toFixed(2)
+
+        console.warn(`\n✅ Indexing complete in ${durationSec}s`)
+        console.warn(`   Files scanned: ${String(stats.filesScanned)}`)
+        console.warn(`   Files parsed: ${String(stats.filesParsed)}`)
+        console.warn(`   Parse errors: ${String(stats.parseErrors)}`)
+        console.warn(`   Symbols: ${String(symbolIndex.size)}`)
+
+        return {
+            success: true,
+            filesIndexed: stats.filesParsed,
+            filesSkipped: stats.filesScanned - stats.filesParsed,
+            errors: [],
+            duration: stats.timeMs,
+        }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        console.error(`❌ Indexing failed: ${message}`)
+        return {
+            success: false,
+            filesIndexed: 0,
+            filesSkipped: 0,
+            errors: [message],
+            duration: Date.now() - startTime,
+        }
+    } finally {
+        if (redisClient) {
+            await redisClient.disconnect()
+        }
+    }
+}

packages/ipuaro/src/cli/commands/index.ts

@@ -0,0 +1,18 @@
+/**
+ * CLI commands module.
+ */
+
+export { executeStart, type StartOptions, type StartResult } from "./start.js"
+export { executeInit, type InitOptions, type InitResult } from "./init.js"
+export { executeIndex, type IndexResult, type IndexProgressCallback } from "./index-cmd.js"
+export {
+    runOnboarding,
+    checkRedis,
+    checkOllama,
+    checkModel,
+    checkProjectSize,
+    pullModel,
+    type OnboardingResult,
+    type OnboardingOptions,
+} from "./onboarding.js"
+export { registerAllTools } from "./tools-setup.js"

packages/ipuaro/src/cli/commands/init.ts

@@ -0,0 +1,114 @@
+/**
+ * Init command implementation.
+ * Creates .ipuaro.json configuration file.
+ */
+
+import * as fs from "node:fs/promises"
+import * as path from "node:path"
+
+/**
+ * Default configuration template for .ipuaro.json
+ */
+const CONFIG_TEMPLATE = {
+    $schema: "https://raw.githubusercontent.com/samiyev/puaros/main/packages/ipuaro/schema.json",
+    redis: {
+        host: "localhost",
+        port: 6379,
+        db: 0,
+    },
+    llm: {
+        model: "qwen2.5-coder:7b-instruct",
+        temperature: 0.1,
+        host: "http://localhost:11434",
+    },
+    project: {
+        ignorePatterns: [],
+    },
+    edit: {
+        autoApply: false,
+    },
+}
+
+/**
+ * Options for init command.
+ */
+export interface InitOptions {
+    force?: boolean
+}
+
+/**
+ * Result of init command.
+ */
+export interface InitResult {
+    success: boolean
+    filePath?: string
+    error?: string
+    skipped?: boolean
+}
+
+/**
+ * Execute the init command.
+ * Creates a .ipuaro.json file in the specified directory.
+ */
+export async function executeInit(
+    projectPath = ".",
+    options: InitOptions = {},
+): Promise<InitResult> {
+    const resolvedPath = path.resolve(projectPath)
+    const configPath = path.join(resolvedPath, ".ipuaro.json")
+
+    try {
+        const exists = await fileExists(configPath)
+
+        if (exists && !options.force) {
+            console.warn(`⚠️  Configuration file already exists: ${configPath}`)
+            console.warn("   Use --force to overwrite.")
+            return {
+                success: true,
+                skipped: true,
+                filePath: configPath,
+            }
+        }
+
+        const dirExists = await fileExists(resolvedPath)
+        if (!dirExists) {
+            await fs.mkdir(resolvedPath, { recursive: true })
+        }
+
+        const content = JSON.stringify(CONFIG_TEMPLATE, null, 4)
+        await fs.writeFile(configPath, content, "utf-8")
+
+        console.warn(`✅ Created ${configPath}`)
+        console.warn("\nConfiguration options:")
+        console.warn("  redis.host     - Redis server host (default: localhost)")
+        console.warn("  redis.port     - Redis server port (default: 6379)")
+        console.warn("  llm.model      - Ollama model name (default: qwen2.5-coder:7b-instruct)")
+        console.warn("  llm.temperature - LLM temperature (default: 0.1)")
+        console.warn("  edit.autoApply - Auto-apply edits without confirmation (default: false)")
+        console.warn("\nRun `ipuaro` to start the AI agent.")
+
+        return {
+            success: true,
+            filePath: configPath,
+        }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        console.error(`❌ Failed to create configuration: ${message}`)
+        return {
+            success: false,
+            error: message,
+        }
+    }
+}
+
+/**
+ * Check if a file or directory exists.
+ */
+async function fileExists(filePath: string): Promise<boolean> {
+    try {
+        await fs.access(filePath)
+        return true
+    } catch {
+        return false
+    }
+}

packages/ipuaro/src/cli/commands/onboarding.ts

@@ -0,0 +1,290 @@
+/**
+ * Onboarding checks for CLI.
+ * Validates environment before starting ipuaro.
+ */
+
+import { RedisClient } from "../../infrastructure/storage/RedisClient.js"
+import { OllamaClient } from "../../infrastructure/llm/OllamaClient.js"
+import { FileScanner } from "../../infrastructure/indexer/FileScanner.js"
+import type { LLMConfig, RedisConfig } from "../../shared/constants/config.js"
+
+/**
+ * Result of onboarding checks.
+ */
+export interface OnboardingResult {
+    success: boolean
+    redisOk: boolean
+    ollamaOk: boolean
+    modelOk: boolean
+    projectOk: boolean
+    fileCount: number
+    errors: string[]
+    warnings: string[]
+}
+
+/**
+ * Options for onboarding checks.
+ */
+export interface OnboardingOptions {
+    redisConfig: RedisConfig
+    llmConfig: LLMConfig
+    projectPath: string
+    maxFiles?: number
+    skipRedis?: boolean
+    skipOllama?: boolean
+    skipModel?: boolean
+    skipProject?: boolean
+}
+
+const DEFAULT_MAX_FILES = 10_000
+
+/**
+ * Check Redis availability.
+ */
+export async function checkRedis(config: RedisConfig): Promise<{
+    ok: boolean
+    error?: string
+}> {
+    const client = new RedisClient(config)
+
+    try {
+        await client.connect()
+        const pingOk = await client.ping()
+        await client.disconnect()
+
+        if (!pingOk) {
+            return {
+                ok: false,
+                error: "Redis ping failed. Server may be overloaded.",
+            }
+        }
+
+        return { ok: true }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        return {
+            ok: false,
+            error: `Cannot connect to Redis: ${message}
+
+Redis is required for ipuaro to store project indexes and session data.
+
+Install Redis:
+  macOS:   brew install redis && brew services start redis
+  Ubuntu:  sudo apt install redis-server && sudo systemctl start redis
+  Docker:  docker run -d -p 6379:6379 redis`,
+        }
+    }
+}
+
+/**
+ * Check Ollama availability.
+ */
+export async function checkOllama(config: LLMConfig): Promise<{
+    ok: boolean
+    error?: string
+}> {
+    const client = new OllamaClient(config)
+
+    try {
+        const available = await client.isAvailable()
+
+        if (!available) {
+            return {
+                ok: false,
+                error: `Cannot connect to Ollama at ${config.host}
+
+Ollama is required for ipuaro to process your requests using local LLMs.
+
+Install Ollama:
+  macOS:   brew install ollama && ollama serve
+  Linux:   curl -fsSL https://ollama.com/install.sh | sh && ollama serve
+  Manual:  https://ollama.com/download
+
+After installing, ensure Ollama is running with: ollama serve`,
+            }
+        }
+
+        return { ok: true }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        return {
+            ok: false,
+            error: `Ollama check failed: ${message}`,
+        }
+    }
+}
+
+/**
+ * Check model availability.
+ */
+export async function checkModel(config: LLMConfig): Promise<{
+    ok: boolean
+    needsPull: boolean
+    error?: string
+}> {
+    const client = new OllamaClient(config)
+
+    try {
+        const hasModel = await client.hasModel(config.model)
+
+        if (!hasModel) {
+            return {
+                ok: false,
+                needsPull: true,
+                error: `Model "${config.model}" is not installed.
+
+Would you like to pull it? This may take a few minutes.
+Run: ollama pull ${config.model}`,
+            }
+        }
+
+        return { ok: true, needsPull: false }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        return {
+            ok: false,
+            needsPull: false,
+            error: `Model check failed: ${message}`,
+        }
+    }
+}
+
+/**
+ * Pull model from Ollama.
+ */
+export async function pullModel(
+    config: LLMConfig,
+    onProgress?: (status: string) => void,
+): Promise<{ ok: boolean; error?: string }> {
+    const client = new OllamaClient(config)
+
+    try {
+        onProgress?.(`Pulling model "${config.model}"...`)
+        await client.pullModel(config.model)
+        onProgress?.(`Model "${config.model}" pulled successfully.`)
+        return { ok: true }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        return {
+            ok: false,
+            error: `Failed to pull model: ${message}`,
+        }
+    }
+}
+
+/**
+ * Check project size.
+ */
+export async function checkProjectSize(
+    projectPath: string,
+    maxFiles: number = DEFAULT_MAX_FILES,
+): Promise<{
+    ok: boolean
+    fileCount: number
+    warning?: string
+}> {
+    const scanner = new FileScanner()
+
+    try {
+        const files = await scanner.scanAll(projectPath)
+        const fileCount = files.length
+
+        if (fileCount > maxFiles) {
+            return {
+                ok: true,
+                fileCount,
+                warning: `Project has ${fileCount.toLocaleString()} files (>${maxFiles.toLocaleString()}).
+This may take a while to index and use more memory.
+
+Consider:
+  1. Running ipuaro in a subdirectory: ipuaro ./src
+  2. Adding patterns to .gitignore to exclude unnecessary files
+  3. Using a smaller project for better performance`,
+            }
+        }
+
+        if (fileCount === 0) {
+            return {
+                ok: false,
+                fileCount: 0,
+                warning: `No supported files found in "${projectPath}".
+
+ipuaro supports: .ts, .tsx, .js, .jsx, .json, .yaml, .yml
+
+Ensure you're running ipuaro in a project directory with source files.`,
+            }
+        }
+
+        return { ok: true, fileCount }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        return {
+            ok: false,
+            fileCount: 0,
+            warning: `Failed to scan project: ${message}`,
+        }
+    }
+}
+
+/**
+ * Run all onboarding checks.
+ */
+export async function runOnboarding(options: OnboardingOptions): Promise<OnboardingResult> {
+    const errors: string[] = []
+    const warnings: string[] = []
+    const maxFiles = options.maxFiles ?? DEFAULT_MAX_FILES
+
+    let redisOk = true
+    let ollamaOk = true
+    let modelOk = true
+    let projectOk = true
+    let fileCount = 0
+
+    if (!options.skipRedis) {
+        const redisResult = await checkRedis(options.redisConfig)
+        redisOk = redisResult.ok
+        if (!redisOk && redisResult.error) {
+            errors.push(redisResult.error)
+        }
+    }
+
+    if (!options.skipOllama) {
+        const ollamaResult = await checkOllama(options.llmConfig)
+        ollamaOk = ollamaResult.ok
+        if (!ollamaOk && ollamaResult.error) {
+            errors.push(ollamaResult.error)
+        }
+    }
+
+    if (!options.skipModel && ollamaOk) {
+        const modelResult = await checkModel(options.llmConfig)
+        modelOk = modelResult.ok
+        if (!modelOk && modelResult.error) {
+            errors.push(modelResult.error)
+        }
+    }
+
+    if (!options.skipProject) {
+        const projectResult = await checkProjectSize(options.projectPath, maxFiles)
+        projectOk = projectResult.ok
+        fileCount = projectResult.fileCount
+        if (projectResult.warning) {
+            if (projectResult.ok) {
+                warnings.push(projectResult.warning)
+            } else {
+                errors.push(projectResult.warning)
+            }
+        }
+    }
+
+    return {
+        success: redisOk && ollamaOk && modelOk && projectOk && errors.length === 0,
+        redisOk,
+        ollamaOk,
+        modelOk,
+        projectOk,
+        fileCount,
+        errors,
+        warnings,
+    }
+}

packages/ipuaro/src/cli/commands/start.ts

@@ -0,0 +1,162 @@
+/**
+ * Start command implementation.
+ * Launches the ipuaro TUI.
+ */
+
+import * as path from "node:path"
+import * as readline from "node:readline"
+import { render } from "ink"
+import React from "react"
+import { App, type AppDependencies } from "../../tui/App.js"
+import { RedisClient } from "../../infrastructure/storage/RedisClient.js"
+import { RedisStorage } from "../../infrastructure/storage/RedisStorage.js"
+import { RedisSessionStorage } from "../../infrastructure/storage/RedisSessionStorage.js"
+import { OllamaClient } from "../../infrastructure/llm/OllamaClient.js"
+import { ToolRegistry } from "../../infrastructure/tools/registry.js"
+import { generateProjectName } from "../../infrastructure/storage/schema.js"
+import { type Config, DEFAULT_CONFIG } from "../../shared/constants/config.js"
+import { checkModel, pullModel, runOnboarding } from "./onboarding.js"
+import { registerAllTools } from "./tools-setup.js"
+
+/**
+ * Options for start command.
+ */
+export interface StartOptions {
+    autoApply?: boolean
+    model?: string
+}
+
+/**
+ * Result of start command.
+ */
+export interface StartResult {
+    success: boolean
+    error?: string
+}
+
+/**
+ * Execute the start command.
+ */
+export async function executeStart(
+    projectPath: string,
+    options: StartOptions,
+    config: Config = DEFAULT_CONFIG,
+): Promise<StartResult> {
+    const resolvedPath = path.resolve(projectPath)
+    const projectName = generateProjectName(resolvedPath)
+
+    const llmConfig = {
+        ...config.llm,
+        model: options.model ?? config.llm.model,
+    }
+
+    console.warn("🔍 Running pre-flight checks...\n")
+
+    const onboardingResult = await runOnboarding({
+        redisConfig: config.redis,
+        llmConfig,
+        projectPath: resolvedPath,
+    })
+
+    for (const warning of onboardingResult.warnings) {
+        console.warn(`⚠️  ${warning}\n`)
+    }
+
+    if (!onboardingResult.success) {
+        for (const error of onboardingResult.errors) {
+            console.error(`❌ ${error}\n`)
+        }
+
+        if (!onboardingResult.modelOk && onboardingResult.ollamaOk) {
+            const shouldPull = await promptYesNo(
+                `Would you like to pull "${llmConfig.model}"? (y/n): `,
+            )
+
+            if (shouldPull) {
+                const pullResult = await pullModel(llmConfig, console.warn)
+                if (!pullResult.ok) {
+                    console.error(`❌ ${pullResult.error ?? "Unknown error"}`)
+                    return { success: false, error: pullResult.error }
+                }
+
+                const recheckModel = await checkModel(llmConfig)
+                if (!recheckModel.ok) {
+                    console.error("❌ Model still not available after pull.")
+                    return { success: false, error: "Model pull failed" }
+                }
+            } else {
+                return { success: false, error: "Model not available" }
+            }
+        } else {
+            return {
+                success: false,
+                error: onboardingResult.errors.join("\n"),
+            }
+        }
+    }
+
+    console.warn(`✅ All checks passed. Found ${String(onboardingResult.fileCount)} files.\n`)
+    console.warn("🚀 Starting ipuaro...\n")
+
+    const redisClient = new RedisClient(config.redis)
+
+    try {
+        await redisClient.connect()
+
+        const storage = new RedisStorage(redisClient, projectName)
+        const sessionStorage = new RedisSessionStorage(redisClient)
+        const llm = new OllamaClient(llmConfig)
+        const tools = new ToolRegistry()
+
+        registerAllTools(tools)
+
+        const deps: AppDependencies = {
+            storage,
+            sessionStorage,
+            llm,
+            tools,
+        }
+
+        const handleExit = (): void => {
+            void redisClient.disconnect()
+        }
+
+        const { waitUntilExit } = render(
+            React.createElement(App, {
+                projectPath: resolvedPath,
+                autoApply: options.autoApply ?? config.edit.autoApply,
+                deps,
+                onExit: handleExit,
+            }),
+        )
+
+        await waitUntilExit()
+        await redisClient.disconnect()
+
+        return { success: true }
+    } catch (error) {
+        const message = error instanceof Error ? error.message : String(error)
+        console.error(`❌ Failed to start ipuaro: ${message}`)
+        await redisClient.disconnect()
+        return { success: false, error: message }
+    }
+}
+
+/**
+ * Simple yes/no prompt for CLI.
+ */
+async function promptYesNo(question: string): Promise<boolean> {
+    return new Promise((resolve) => {
+        process.stdout.write(question)
+
+        const rl = readline.createInterface({
+            input: process.stdin,
+            output: process.stdout,
+        })
+
+        rl.once("line", (answer: string) => {
+            rl.close()
+            resolve(answer.toLowerCase() === "y" || answer.toLowerCase() === "yes")
+        })
+    })
+}

packages/ipuaro/src/cli/commands/tools-setup.ts

@@ -0,0 +1,59 @@
+/**
+ * Tool registration helper for CLI.
+ * Registers all 18 tools with the tool registry.
+ */
+
+import type { IToolRegistry } from "../../application/interfaces/IToolRegistry.js"
+
+import { GetLinesTool } from "../../infrastructure/tools/read/GetLinesTool.js"
+import { GetFunctionTool } from "../../infrastructure/tools/read/GetFunctionTool.js"
+import { GetClassTool } from "../../infrastructure/tools/read/GetClassTool.js"
+import { GetStructureTool } from "../../infrastructure/tools/read/GetStructureTool.js"
+
+import { EditLinesTool } from "../../infrastructure/tools/edit/EditLinesTool.js"
+import { CreateFileTool } from "../../infrastructure/tools/edit/CreateFileTool.js"
+import { DeleteFileTool } from "../../infrastructure/tools/edit/DeleteFileTool.js"
+
+import { FindReferencesTool } from "../../infrastructure/tools/search/FindReferencesTool.js"
+import { FindDefinitionTool } from "../../infrastructure/tools/search/FindDefinitionTool.js"
+
+import { GetDependenciesTool } from "../../infrastructure/tools/analysis/GetDependenciesTool.js"
+import { GetDependentsTool } from "../../infrastructure/tools/analysis/GetDependentsTool.js"
+import { GetComplexityTool } from "../../infrastructure/tools/analysis/GetComplexityTool.js"
+import { GetTodosTool } from "../../infrastructure/tools/analysis/GetTodosTool.js"
+
+import { GitStatusTool } from "../../infrastructure/tools/git/GitStatusTool.js"
+import { GitDiffTool } from "../../infrastructure/tools/git/GitDiffTool.js"
+import { GitCommitTool } from "../../infrastructure/tools/git/GitCommitTool.js"
+
+import { RunCommandTool } from "../../infrastructure/tools/run/RunCommandTool.js"
+import { RunTestsTool } from "../../infrastructure/tools/run/RunTestsTool.js"
+
+/**
+ * Register all 18 tools with the tool registry.
+ */
+export function registerAllTools(registry: IToolRegistry): void {
+    registry.register(new GetLinesTool())
+    registry.register(new GetFunctionTool())
+    registry.register(new GetClassTool())
+    registry.register(new GetStructureTool())
+
+    registry.register(new EditLinesTool())
+    registry.register(new CreateFileTool())
+    registry.register(new DeleteFileTool())
+
+    registry.register(new FindReferencesTool())
+    registry.register(new FindDefinitionTool())
+
+    registry.register(new GetDependenciesTool())
+    registry.register(new GetDependentsTool())
+    registry.register(new GetComplexityTool())
+    registry.register(new GetTodosTool())
+
+    registry.register(new GitStatusTool())
+    registry.register(new GitDiffTool())
+    registry.register(new GitCommitTool())
+
+    registry.register(new RunCommandTool())
+    registry.register(new RunTestsTool())
+}

packages/ipuaro/src/cli/index.ts

@@ -1,44 +1,63 @@
 #!/usr/bin/env node
 
+/**
+ * ipuaro CLI entry point.
+ * Local AI agent for codebase operations with infinite context feeling.
+ */
+
+import { createRequire } from "node:module"
 import { Command } from "commander"
+import { executeStart } from "./commands/start.js"
+import { executeInit } from "./commands/init.js"
+import { executeIndex } from "./commands/index-cmd.js"
+import { loadConfig } from "../shared/config/loader.js"
+
+const require = createRequire(import.meta.url)
+const pkg = require("../../package.json") as { version: string }
 
 const program = new Command()
 
 program
     .name("ipuaro")
     .description("Local AI agent for codebase operations with infinite context feeling")
-    .version("0.1.0")
+    .version(pkg.version)
 
 program
-    .command("start")
+    .command("start", { isDefault: true })
     .description("Start ipuaro TUI in the current directory")
     .argument("[path]", "Project path", ".")
     .option("--auto-apply", "Enable auto-apply mode for edits")
-    .option("--model <name>", "Override LLM model", "qwen2.5-coder:7b-instruct")
-    .action((path: string, options: { autoApply?: boolean; model?: string }) => {
-        const model = options.model ?? "default"
-        const autoApply = options.autoApply ?? false
-        console.warn(`Starting ipuaro in ${path}...`)
-        console.warn(`Model: ${model}`)
-        console.warn(`Auto-apply: ${autoApply ? "enabled" : "disabled"}`)
-        console.warn("\nNot implemented yet. Coming in version 0.11.0!")
+    .option("--model <name>", "Override LLM model")
+    .action(async (projectPath: string, options: { autoApply?: boolean; model?: string }) => {
+        const config = loadConfig(projectPath)
+        const result = await executeStart(projectPath, options, config)
+        if (!result.success) {
+            process.exit(1)
+        }
     })
 
 program
     .command("init")
     .description("Create .ipuaro.json config file")
-    .action(() => {
-        console.warn("Creating .ipuaro.json...")
-        console.warn("\nNot implemented yet. Coming in version 0.17.0!")
+    .argument("[path]", "Project path", ".")
+    .option("--force", "Overwrite existing config file")
+    .action(async (projectPath: string, options: { force?: boolean }) => {
+        const result = await executeInit(projectPath, options)
+        if (!result.success) {
+            process.exit(1)
+        }
     })
 
 program
     .command("index")
     .description("Index project without starting TUI")
     .argument("[path]", "Project path", ".")
-    .action((path: string) => {
-        console.warn(`Indexing ${path}...`)
-        console.warn("\nNot implemented yet. Coming in version 0.3.0!")
+    .action(async (projectPath: string) => {
+        const config = loadConfig(projectPath)
+        const result = await executeIndex(projectPath, config)
+        if (!result.success) {
+            process.exit(1)
+        }
     })
 
 program.parse()

packages/ipuaro/src/domain/entities/Session.ts

@@ -94,6 +94,12 @@ export class Session {
         }
     }
 
+    truncateHistory(maxMessages: number): void {
+        if (this.history.length > maxMessages) {
+            this.history = this.history.slice(-maxMessages)
+        }
+    }
+
     clearHistory(): void {
         this.history = []
         this.context = {

packages/ipuaro/src/domain/services/IIndexer.ts

@@ -21,6 +21,7 @@ export interface ScanResult {
     type: "file" | "directory" | "symlink"
     size: number
     lastModified: number
+    symlinkTarget?: string
 }
 
 /**
@@ -46,7 +47,7 @@ export interface IIndexer {
     /**
      * Parse file content into AST.
      */
-    parseFile(content: string, language: "ts" | "tsx" | "js" | "jsx"): FileAST
+    parseFile(content: string, language: "ts" | "tsx" | "js" | "jsx" | "json" | "yaml"): FileAST
 
     /**
      * Analyze file and compute metadata.

packages/ipuaro/src/domain/services/ILLMClient.ts

@@ -1,26 +1,6 @@
 import type { ChatMessage } from "../value-objects/ChatMessage.js"
 import type { ToolCall } from "../value-objects/ToolCall.js"
 
-/**
- * Tool parameter definition for LLM.
- */
-export interface ToolParameter {
-    name: string
-    type: "string" | "number" | "boolean" | "array" | "object"
-    description: string
-    required: boolean
-    enum?: string[]
-}
-
-/**
- * Tool definition for LLM function calling.
- */
-export interface ToolDef {
-    name: string
-    description: string
-    parameters: ToolParameter[]
-}
-
 /**
  * Response from LLM.
  */
@@ -42,12 +22,16 @@ export interface LLMResponse {
 /**
  * LLM client service interface (port).
  * Abstracts the LLM provider.
+ *
+ * Tool definitions should be included in the system prompt as XML format,
+ * not passed as a separate parameter.
  */
 export interface ILLMClient {
     /**
      * Send messages to LLM and get response.
+     * Tool calls are extracted from the response content using XML parsing.
      */
-    chat(messages: ChatMessage[], tools?: ToolDef[]): Promise<LLMResponse>
+    chat(messages: ChatMessage[]): Promise<LLMResponse>
 
     /**
      * Count tokens in text.

packages/ipuaro/src/domain/value-objects/FileAST.ts

@@ -52,6 +52,8 @@ export interface FunctionInfo {
     isExported: boolean
     /** Return type (if available) */
     returnType?: string
+    /** Decorators applied to the function (e.g., ["@Get(':id')", "@Auth()"]) */
+    decorators?: string[]
 }
 
 export interface MethodInfo {
@@ -69,6 +71,8 @@ export interface MethodInfo {
     visibility: "public" | "private" | "protected"
     /** Whether it's static */
     isStatic: boolean
+    /** Decorators applied to the method (e.g., ["@Get(':id')", "@UseGuards(AuthGuard)"]) */
+    decorators?: string[]
 }
 
 export interface PropertyInfo {
@@ -105,6 +109,8 @@ export interface ClassInfo {
     isExported: boolean
     /** Whether class is abstract */
     isAbstract: boolean
+    /** Decorators applied to the class (e.g., ["@Controller('users')", "@Injectable()"]) */
+    decorators?: string[]
 }
 
 export interface InterfaceInfo {
@@ -129,6 +135,30 @@ export interface TypeAliasInfo {
     line: number
     /** Whether it's exported */
     isExported: boolean
+    /** Type definition (e.g., "string", "User & Admin", "{ id: string }") */
+    definition?: string
+}
+
+export interface EnumMemberInfo {
+    /** Member name */
+    name: string
+    /** Member value (string or number, if specified) */
+    value?: string | number
+}
+
+export interface EnumInfo {
+    /** Enum name */
+    name: string
+    /** Start line number */
+    lineStart: number
+    /** End line number */
+    lineEnd: number
+    /** Enum members with values */
+    members: EnumMemberInfo[]
+    /** Whether it's exported */
+    isExported: boolean
+    /** Whether it's a const enum */
+    isConst: boolean
 }
 
 export interface FileAST {
@@ -144,6 +174,8 @@ export interface FileAST {
     interfaces: InterfaceInfo[]
     /** Type alias declarations */
     typeAliases: TypeAliasInfo[]
+    /** Enum declarations */
+    enums: EnumInfo[]
     /** Whether parsing encountered errors */
     parseError: boolean
     /** Parse error message if any */
@@ -158,6 +190,7 @@ export function createEmptyFileAST(): FileAST {
         classes: [],
         interfaces: [],
         typeAliases: [],
+        enums: [],
         parseError: false,
     }
 }

packages/ipuaro/src/domain/value-objects/FileMeta.ts

@@ -26,6 +26,12 @@ export interface FileMeta {
     isEntryPoint: boolean
     /** File type classification */
     fileType: "source" | "test" | "config" | "types" | "unknown"
+    /** Impact score (0-100): percentage of codebase that depends on this file */
+    impactScore: number
+    /** Count of files that depend on this file transitively (including indirect dependents) */
+    transitiveDepCount: number
+    /** Count of files this file depends on transitively (including indirect dependencies) */
+    transitiveDepByCount: number
 }
 
 export function createFileMeta(partial: Partial<FileMeta> = {}): FileMeta {
@@ -41,6 +47,9 @@ export function createFileMeta(partial: Partial<FileMeta> = {}): FileMeta {
         isHub: false,
         isEntryPoint: false,
         fileType: "unknown",
+        impactScore: 0,
+        transitiveDepCount: 0,
+        transitiveDepByCount: 0,
         ...partial,
     }
 }
@@ -48,3 +57,20 @@ export function createFileMeta(partial: Partial<FileMeta> = {}): FileMeta {
 export function isHubFile(dependentCount: number): boolean {
     return dependentCount > 5
 }
+
+/**
+ * Calculate impact score based on number of dependents and total files.
+ * Impact score represents what percentage of the codebase depends on this file.
+ * @param dependentCount - Number of files that depend on this file
+ * @param totalFiles - Total number of files in the project
+ * @returns Impact score from 0 to 100
+ */
+export function calculateImpactScore(dependentCount: number, totalFiles: number): number {
+    if (totalFiles <= 1) {
+        return 0
+    }
+    // Exclude the file itself from the total
+    const maxPossibleDependents = totalFiles - 1
+    const score = (dependentCount / maxPossibleDependents) * 100
+    return Math.round(Math.min(100, score))
+}

packages/ipuaro/src/infrastructure/index.ts

@@ -3,3 +3,4 @@ export * from "./storage/index.js"
 export * from "./indexer/index.js"
 export * from "./llm/index.js"
 export * from "./tools/index.js"
+export * from "./security/index.js"

packages/ipuaro/src/infrastructure/indexer/ASTParser.ts

@@ -2,8 +2,11 @@ import { builtinModules } from "node:module"
 import Parser from "tree-sitter"
 import TypeScript from "tree-sitter-typescript"
 import JavaScript from "tree-sitter-javascript"
+import JSON from "tree-sitter-json"
+import * as yamlParser from "yaml"
 import {
     createEmptyFileAST,
+    type EnumMemberInfo,
     type ExportInfo,
     type FileAST,
     type ImportInfo,
@@ -13,7 +16,7 @@ import {
 } from "../../domain/value-objects/FileAST.js"
 import { FieldName, NodeType } from "./tree-sitter-types.js"
 
-type Language = "ts" | "tsx" | "js" | "jsx"
+type Language = "ts" | "tsx" | "js" | "jsx" | "json" | "yaml"
 type SyntaxNode = Parser.SyntaxNode
 
 /**
@@ -39,12 +42,20 @@ export class ASTParser {
         jsParser.setLanguage(JavaScript)
         this.parsers.set("js", jsParser)
         this.parsers.set("jsx", jsParser)
+
+        const jsonParser = new Parser()
+        jsonParser.setLanguage(JSON)
+        this.parsers.set("json", jsonParser)
     }
 
     /**
      * Parse source code and extract AST information.
      */
     parse(content: string, language: Language): FileAST {
+        if (language === "yaml") {
+            return this.parseYAML(content)
+        }
+
         const parser = this.parsers.get(language)
         if (!parser) {
             return {
@@ -75,8 +86,77 @@ export class ASTParser {
         }
     }
 
+    /**
+     * Parse YAML content using yaml package.
+     */
+    private parseYAML(content: string): FileAST {
+        const ast = createEmptyFileAST()
+
+        try {
+            const doc = yamlParser.parseDocument(content)
+
+            if (doc.errors.length > 0) {
+                return {
+                    ...createEmptyFileAST(),
+                    parseError: true,
+                    parseErrorMessage: doc.errors[0].message,
+                }
+            }
+
+            const contents = doc.contents
+
+            if (yamlParser.isSeq(contents)) {
+                ast.exports.push({
+                    name: "(array)",
+                    line: 1,
+                    isDefault: false,
+                    kind: "variable",
+                })
+            } else if (yamlParser.isMap(contents)) {
+                for (const item of contents.items) {
+                    if (yamlParser.isPair(item) && yamlParser.isScalar(item.key)) {
+                        const keyRange = item.key.range
+                        const line = keyRange ? this.getLineFromOffset(content, keyRange[0]) : 1
+                        ast.exports.push({
+                            name: String(item.key.value),
+                            line,
+                            isDefault: false,
+                            kind: "variable",
+                        })
+                    }
+                }
+            }
+
+            return ast
+        } catch (error) {
+            return {
+                ...createEmptyFileAST(),
+                parseError: true,
+                parseErrorMessage: error instanceof Error ? error.message : "YAML parse error",
+            }
+        }
+    }
+
+    /**
+     * Get line number from character offset.
+     */
+    private getLineFromOffset(content: string, offset: number): number {
+        let line = 1
+        for (let i = 0; i < offset && i < content.length; i++) {
+            if (content[i] === "\n") {
+                line++
+            }
+        }
+        return line
+    }
+
     private extractAST(root: SyntaxNode, language: Language): FileAST {
         const ast = createEmptyFileAST()
+
+        if (language === "json") {
+            return this.extractJSONStructure(root, ast)
+        }
+
         const isTypeScript = language === "ts" || language === "tsx"
 
         for (const child of root.children) {
@@ -113,6 +193,11 @@ export class ASTParser {
                     this.extractTypeAlias(node, ast, false)
                 }
                 break
+            case NodeType.ENUM_DECLARATION:
+                if (isTypeScript) {
+                    this.extractEnum(node, ast, false)
+                }
+                break
         }
     }
 
@@ -179,13 +264,15 @@ export class ASTParser {
         const declaration = node.childForFieldName(FieldName.DECLARATION)
 
         if (declaration) {
+            const decorators = this.extractDecoratorsFromSiblings(declaration)
+
             switch (declaration.type) {
                 case NodeType.FUNCTION_DECLARATION:
-                    this.extractFunction(declaration, ast, true)
+                    this.extractFunction(declaration, ast, true, decorators)
                     this.addExportInfo(ast, declaration, "function", isDefault)
                     break
                 case NodeType.CLASS_DECLARATION:
-                    this.extractClass(declaration, ast, true)
+                    this.extractClass(declaration, ast, true, decorators)
                     this.addExportInfo(ast, declaration, "class", isDefault)
                     break
                 case NodeType.INTERFACE_DECLARATION:
@@ -196,6 +283,10 @@ export class ASTParser {
                     this.extractTypeAlias(declaration, ast, true)
                     this.addExportInfo(ast, declaration, "type", isDefault)
                     break
+                case NodeType.ENUM_DECLARATION:
+                    this.extractEnum(declaration, ast, true)
+                    this.addExportInfo(ast, declaration, "type", isDefault)
+                    break
                 case NodeType.LEXICAL_DECLARATION:
                     this.extractLexicalDeclaration(declaration, ast, true)
                     break
@@ -220,7 +311,12 @@ export class ASTParser {
         }
     }
 
-    private extractFunction(node: SyntaxNode, ast: FileAST, isExported: boolean): void {
+    private extractFunction(
+        node: SyntaxNode,
+        ast: FileAST,
+        isExported: boolean,
+        externalDecorators: string[] = [],
+    ): void {
         const nameNode = node.childForFieldName(FieldName.NAME)
         if (!nameNode) {
             return
@@ -230,6 +326,9 @@ export class ASTParser {
         const isAsync = node.children.some((c) => c.type === NodeType.ASYNC)
         const returnTypeNode = node.childForFieldName(FieldName.RETURN_TYPE)
 
+        const nodeDecorators = this.extractNodeDecorators(node)
+        const decorators = [...externalDecorators, ...nodeDecorators]
+
         ast.functions.push({
             name: nameNode.text,
             lineStart: node.startPosition.row + 1,
@@ -238,6 +337,7 @@ export class ASTParser {
             isAsync,
             isExported,
             returnType: returnTypeNode?.text?.replace(/^:\s*/, ""),
+            decorators,
         })
     }
 
@@ -253,6 +353,7 @@ export class ASTParser {
                 ) {
                     const params = this.extractParameters(valueNode)
                     const isAsync = valueNode.children.some((c) => c.type === NodeType.ASYNC)
+                    const returnTypeNode = valueNode.childForFieldName(FieldName.RETURN_TYPE)
 
                     ast.functions.push({
                         name: nameNode?.text ?? "",
@@ -261,6 +362,8 @@ export class ASTParser {
                         params,
                         isAsync,
                         isExported,
+                        returnType: returnTypeNode?.text?.replace(/^:\s*/, ""),
+                        decorators: [],
                     })
 
                     if (isExported) {
@@ -283,7 +386,12 @@ export class ASTParser {
         }
     }
 
-    private extractClass(node: SyntaxNode, ast: FileAST, isExported: boolean): void {
+    private extractClass(
+        node: SyntaxNode,
+        ast: FileAST,
+        isExported: boolean,
+        externalDecorators: string[] = [],
+    ): void {
         const nameNode = node.childForFieldName(FieldName.NAME)
         if (!nameNode) {
             return
@@ -294,14 +402,19 @@ export class ASTParser {
         const properties: PropertyInfo[] = []
 
         if (body) {
+            let pendingDecorators: string[] = []
             for (const member of body.children) {
-                if (member.type === NodeType.METHOD_DEFINITION) {
-                    methods.push(this.extractMethod(member))
+                if (member.type === NodeType.DECORATOR) {
+                    pendingDecorators.push(this.formatDecorator(member))
+                } else if (member.type === NodeType.METHOD_DEFINITION) {
+                    methods.push(this.extractMethod(member, pendingDecorators))
+                    pendingDecorators = []
                 } else if (
                     member.type === NodeType.PUBLIC_FIELD_DEFINITION ||
                     member.type === NodeType.FIELD_DEFINITION
                 ) {
                     properties.push(this.extractProperty(member))
+                    pendingDecorators = []
                 }
             }
         }
@@ -309,6 +422,9 @@ export class ASTParser {
         const { extendsName, implementsList } = this.extractClassHeritage(node)
         const isAbstract = node.children.some((c) => c.type === NodeType.ABSTRACT)
 
+        const nodeDecorators = this.extractNodeDecorators(node)
+        const decorators = [...externalDecorators, ...nodeDecorators]
+
         ast.classes.push({
             name: nameNode.text,
             lineStart: node.startPosition.row + 1,
@@ -319,6 +435,7 @@ export class ASTParser {
             implements: implementsList,
             isExported,
             isAbstract,
+            decorators,
         })
     }
 
@@ -372,7 +489,7 @@ export class ASTParser {
         }
     }
 
-    private extractMethod(node: SyntaxNode): MethodInfo {
+    private extractMethod(node: SyntaxNode, decorators: string[] = []): MethodInfo {
         const nameNode = node.childForFieldName(FieldName.NAME)
         const params = this.extractParameters(node)
         const isAsync = node.children.some((c) => c.type === NodeType.ASYNC)
@@ -394,6 +511,7 @@ export class ASTParser {
             isAsync,
             visibility,
             isStatic,
+            decorators,
         }
     }
 
@@ -473,13 +591,86 @@ export class ASTParser {
             return
         }
 
+        const valueNode = node.childForFieldName(FieldName.VALUE)
+        const definition = valueNode?.text
+
         ast.typeAliases.push({
             name: nameNode.text,
             line: node.startPosition.row + 1,
             isExported,
+            definition,
         })
     }
 
+    private extractEnum(node: SyntaxNode, ast: FileAST, isExported: boolean): void {
+        const nameNode = node.childForFieldName(FieldName.NAME)
+        if (!nameNode) {
+            return
+        }
+
+        const body = node.childForFieldName(FieldName.BODY)
+        const members: EnumMemberInfo[] = []
+
+        if (body) {
+            for (const child of body.children) {
+                if (child.type === NodeType.ENUM_ASSIGNMENT) {
+                    const memberName = child.childForFieldName(FieldName.NAME)
+                    const memberValue = child.childForFieldName(FieldName.VALUE)
+                    if (memberName) {
+                        members.push({
+                            name: memberName.text,
+                            value: this.parseEnumValue(memberValue),
+                        })
+                    }
+                } else if (
+                    child.type === NodeType.IDENTIFIER ||
+                    child.type === NodeType.PROPERTY_IDENTIFIER
+                ) {
+                    members.push({
+                        name: child.text,
+                        value: undefined,
+                    })
+                }
+            }
+        }
+
+        const isConst = node.children.some((c) => c.text === "const")
+
+        ast.enums.push({
+            name: nameNode.text,
+            lineStart: node.startPosition.row + 1,
+            lineEnd: node.endPosition.row + 1,
+            members,
+            isExported,
+            isConst,
+        })
+    }
+
+    private parseEnumValue(valueNode: SyntaxNode | null): string | number | undefined {
+        if (!valueNode) {
+            return undefined
+        }
+
+        const text = valueNode.text
+
+        if (valueNode.type === "number") {
+            return Number(text)
+        }
+
+        if (valueNode.type === "string") {
+            return this.getStringValue(valueNode)
+        }
+
+        if (valueNode.type === "unary_expression" && text.startsWith("-")) {
+            const num = Number(text)
+            if (!isNaN(num)) {
+                return num
+            }
+        }
+
+        return text
+    }
+
     private extractParameters(node: SyntaxNode): ParameterInfo[] {
         const params: ParameterInfo[] = []
         const paramsNode = node.childForFieldName(FieldName.PARAMETERS)
@@ -528,6 +719,49 @@ export class ASTParser {
         }
     }
 
+    /**
+     * Format a decorator node to a string like "@Get(':id')" or "@Injectable()".
+     */
+    private formatDecorator(node: SyntaxNode): string {
+        return node.text.replace(/\s+/g, " ").trim()
+    }
+
+    /**
+     * Extract decorators that are direct children of a node.
+     * In tree-sitter, decorators are children of the class/function declaration.
+     */
+    private extractNodeDecorators(node: SyntaxNode): string[] {
+        const decorators: string[] = []
+        for (const child of node.children) {
+            if (child.type === NodeType.DECORATOR) {
+                decorators.push(this.formatDecorator(child))
+            }
+        }
+        return decorators
+    }
+
+    /**
+     * Extract decorators from sibling nodes before the current node.
+     * Decorators appear as children before the declaration in export statements.
+     */
+    private extractDecoratorsFromSiblings(node: SyntaxNode): string[] {
+        const decorators: string[] = []
+        const parent = node.parent
+        if (!parent) {
+            return decorators
+        }
+
+        for (const sibling of parent.children) {
+            if (sibling.type === NodeType.DECORATOR) {
+                decorators.push(this.formatDecorator(sibling))
+            } else if (sibling === node) {
+                break
+            }
+        }
+
+        return decorators
+    }
+
     private classifyImport(from: string): ImportInfo["type"] {
         if (from.startsWith(".") || from.startsWith("/")) {
             return "internal"
@@ -548,4 +782,37 @@ export class ASTParser {
         }
         return text
     }
+
+    /**
+     * Extract structure from JSON file.
+     * For JSON files, we extract top-level keys from objects.
+     */
+    private extractJSONStructure(root: SyntaxNode, ast: FileAST): FileAST {
+        for (const child of root.children) {
+            if (child.type === "object") {
+                this.extractJSONKeys(child, ast)
+            }
+        }
+        return ast
+    }
+
+    /**
+     * Extract keys from JSON object.
+     */
+    private extractJSONKeys(node: SyntaxNode, ast: FileAST): void {
+        for (const child of node.children) {
+            if (child.type === "pair") {
+                const keyNode = child.childForFieldName("key")
+                if (keyNode) {
+                    const keyName = this.getStringValue(keyNode)
+                    ast.exports.push({
+                        name: keyName,
+                        line: keyNode.startPosition.row + 1,
+                        isDefault: false,
+                        kind: "variable",
+                    })
+                }
+            }
+        }
+    }
 }

packages/ipuaro/src/infrastructure/indexer/FileScanner.ts

@@ -96,12 +96,27 @@ export class FileScanner {
             const stats = await this.safeStats(fullPath)
 
             if (stats) {
-                yield {
+                const type = stats.isSymbolicLink()
+                    ? "symlink"
+                    : stats.isDirectory()
+                      ? "directory"
+                      : "file"
+
+                const result: ScanResult = {
                     path: relativePath,
-                    type: "file",
+                    type,
                     size: stats.size,
                     lastModified: stats.mtimeMs,
                 }
+
+                if (type === "symlink") {
+                    const target = await this.safeReadlink(fullPath)
+                    if (target) {
+                        result.symlinkTarget = target
+                    }
+                }
+
+                yield result
             }
         }
     }
@@ -127,10 +142,22 @@ export class FileScanner {
 
     /**
      * Safely get file stats without throwing.
+     * Uses lstat to get information about symlinks themselves.
      */
     private async safeStats(filePath: string): Promise<Stats | null> {
         try {
-            return await fs.stat(filePath)
+            return await fs.lstat(filePath)
+        } catch {
+            return null
+        }
+    }
+
+    /**
+     * Safely read symlink target without throwing.
+     */
+    private async safeReadlink(filePath: string): Promise<string | null> {
+        try {
+            return await fs.readlink(filePath)
         } catch {
             return null
         }

packages/ipuaro/src/infrastructure/indexer/MetaAnalyzer.ts

@@ -1,5 +1,6 @@
 import * as path from "node:path"
 import {
+    calculateImpactScore,
     type ComplexityMetrics,
     createFileMeta,
     type FileMeta,
@@ -430,6 +431,7 @@ export class MetaAnalyzer {
 
     /**
      * Batch analyze multiple files.
+     * Computes impact scores and transitive dependencies after all files are analyzed.
      */
     analyzeAll(files: Map<string, { ast: FileAST; content: string }>): Map<string, FileMeta> {
         const allASTs = new Map<string, FileAST>()
@@ -443,6 +445,171 @@ export class MetaAnalyzer {
             results.set(filePath, meta)
         }
 
+        // Compute impact scores now that we know total file count
+        const totalFiles = results.size
+        for (const [, meta] of results) {
+            meta.impactScore = calculateImpactScore(meta.dependents.length, totalFiles)
+        }
+
+        // Compute transitive dependency counts
+        this.computeTransitiveCounts(results)
+
         return results
     }
+
+    /**
+     * Compute transitive dependency counts for all files.
+     * Uses DFS with memoization for efficiency.
+     */
+    computeTransitiveCounts(metas: Map<string, FileMeta>): void {
+        // Memoization caches
+        const transitiveDepCache = new Map<string, Set<string>>()
+        const transitiveDepByCache = new Map<string, Set<string>>()
+
+        // Compute transitive dependents (files that depend on this file, directly or transitively)
+        for (const [filePath, meta] of metas) {
+            const transitiveDeps = this.getTransitiveDependents(filePath, metas, transitiveDepCache)
+            // Exclude the file itself from count (can happen in cycles)
+            meta.transitiveDepCount = transitiveDeps.has(filePath)
+                ? transitiveDeps.size - 1
+                : transitiveDeps.size
+        }
+
+        // Compute transitive dependencies (files this file depends on, directly or transitively)
+        for (const [filePath, meta] of metas) {
+            const transitiveDepsBy = this.getTransitiveDependencies(
+                filePath,
+                metas,
+                transitiveDepByCache,
+            )
+            // Exclude the file itself from count (can happen in cycles)
+            meta.transitiveDepByCount = transitiveDepsBy.has(filePath)
+                ? transitiveDepsBy.size - 1
+                : transitiveDepsBy.size
+        }
+    }
+
+    /**
+     * Get all files that depend on the given file transitively.
+     * Uses DFS with cycle detection. Caching only at the top level.
+     */
+    getTransitiveDependents(
+        filePath: string,
+        metas: Map<string, FileMeta>,
+        cache: Map<string, Set<string>>,
+        visited?: Set<string>,
+    ): Set<string> {
+        // Return cached result if available (only valid for top-level calls)
+        if (!visited) {
+            const cached = cache.get(filePath)
+            if (cached) {
+                return cached
+            }
+        }
+
+        const isTopLevel = !visited
+        if (!visited) {
+            visited = new Set()
+        }
+
+        // Detect cycles
+        if (visited.has(filePath)) {
+            return new Set()
+        }
+
+        visited.add(filePath)
+        const result = new Set<string>()
+
+        const meta = metas.get(filePath)
+        if (!meta) {
+            if (isTopLevel) {
+                cache.set(filePath, result)
+            }
+            return result
+        }
+
+        // Add direct dependents
+        for (const dependent of meta.dependents) {
+            result.add(dependent)
+
+            // Recursively add transitive dependents
+            const transitive = this.getTransitiveDependents(
+                dependent,
+                metas,
+                cache,
+                new Set(visited),
+            )
+            for (const t of transitive) {
+                result.add(t)
+            }
+        }
+
+        // Only cache top-level results (not intermediate results during recursion)
+        if (isTopLevel) {
+            cache.set(filePath, result)
+        }
+        return result
+    }
+
+    /**
+     * Get all files that the given file depends on transitively.
+     * Uses DFS with cycle detection. Caching only at the top level.
+     */
+    getTransitiveDependencies(
+        filePath: string,
+        metas: Map<string, FileMeta>,
+        cache: Map<string, Set<string>>,
+        visited?: Set<string>,
+    ): Set<string> {
+        // Return cached result if available (only valid for top-level calls)
+        if (!visited) {
+            const cached = cache.get(filePath)
+            if (cached) {
+                return cached
+            }
+        }
+
+        const isTopLevel = !visited
+        if (!visited) {
+            visited = new Set()
+        }
+
+        // Detect cycles
+        if (visited.has(filePath)) {
+            return new Set()
+        }
+
+        visited.add(filePath)
+        const result = new Set<string>()
+
+        const meta = metas.get(filePath)
+        if (!meta) {
+            if (isTopLevel) {
+                cache.set(filePath, result)
+            }
+            return result
+        }
+
+        // Add direct dependencies
+        for (const dependency of meta.dependencies) {
+            result.add(dependency)
+
+            // Recursively add transitive dependencies
+            const transitive = this.getTransitiveDependencies(
+                dependency,
+                metas,
+                cache,
+                new Set(visited),
+            )
+            for (const t of transitive) {
+                result.add(t)
+            }
+        }
+
+        // Only cache top-level results (not intermediate results during recursion)
+        if (isTopLevel) {
+            cache.set(filePath, result)
+        }
+        return result
+    }
 }

packages/ipuaro/src/infrastructure/indexer/tree-sitter-types.ts

@@ -16,6 +16,7 @@ export const NodeType = {
     CLASS_DECLARATION: "class_declaration",
     INTERFACE_DECLARATION: "interface_declaration",
     TYPE_ALIAS_DECLARATION: "type_alias_declaration",
+    ENUM_DECLARATION: "enum_declaration",
 
     // Clauses
     IMPORT_CLAUSE: "import_clause",
@@ -37,6 +38,11 @@ export const NodeType = {
     FIELD_DEFINITION: "field_definition",
     PROPERTY_SIGNATURE: "property_signature",
 
+    // Enum members
+    ENUM_BODY: "enum_body",
+    ENUM_ASSIGNMENT: "enum_assignment",
+    PROPERTY_IDENTIFIER: "property_identifier",
+
     // Parameters
     REQUIRED_PARAMETER: "required_parameter",
     OPTIONAL_PARAMETER: "optional_parameter",
@@ -57,6 +63,9 @@ export const NodeType = {
     DEFAULT: "default",
     ACCESSIBILITY_MODIFIER: "accessibility_modifier",
     READONLY: "readonly",
+
+    // Decorators
+    DECORATOR: "decorator",
 } as const
 
 export type NodeTypeValue = (typeof NodeType)[keyof typeof NodeType]

packages/ipuaro/src/infrastructure/llm/OllamaClient.ts

@@ -1,19 +1,17 @@
 import { type Message, Ollama, type Tool } from "ollama"
-import type {
-    ILLMClient,
-    LLMResponse,
-    ToolDef,
-    ToolParameter,
-} from "../../domain/services/ILLMClient.js"
+import type { ILLMClient, LLMResponse } from "../../domain/services/ILLMClient.js"
 import type { ChatMessage } from "../../domain/value-objects/ChatMessage.js"
 import { createToolCall, type ToolCall } from "../../domain/value-objects/ToolCall.js"
 import type { LLMConfig } from "../../shared/constants/config.js"
 import { IpuaroError } from "../../shared/errors/IpuaroError.js"
 import { estimateTokens } from "../../shared/utils/tokens.js"
+import { parseToolCalls } from "./ResponseParser.js"
+import { getOllamaNativeTools } from "./toolDefs.js"
 
 /**
  * Ollama LLM client implementation.
  * Wraps the Ollama SDK for chat completions with tool support.
+ * Supports both XML-based and native Ollama tool calling.
  */
 export class OllamaClient implements ILLMClient {
     private readonly client: Ollama
@@ -22,6 +20,7 @@ export class OllamaClient implements ILLMClient {
     private readonly contextWindow: number
     private readonly temperature: number
     private readonly timeout: number
+    private readonly useNativeTools: boolean
     private abortController: AbortController | null = null
 
     constructor(config: LLMConfig) {
@@ -31,40 +30,25 @@ export class OllamaClient implements ILLMClient {
         this.contextWindow = config.contextWindow
         this.temperature = config.temperature
         this.timeout = config.timeout
+        this.useNativeTools = config.useNativeTools ?? false
     }
 
     /**
      * Send messages to LLM and get response.
+     * Supports both XML-based tool calling and native Ollama tools.
      */
-    async chat(messages: ChatMessage[], tools?: ToolDef[]): Promise<LLMResponse> {
+    async chat(messages: ChatMessage[]): Promise<LLMResponse> {
         const startTime = Date.now()
         this.abortController = new AbortController()
 
         try {
             const ollamaMessages = this.convertMessages(messages)
-            const ollamaTools = tools ? this.convertTools(tools) : undefined
 
-            const response = await this.client.chat({
-                model: this.model,
-                messages: ollamaMessages,
-                tools: ollamaTools,
-                options: {
-                    temperature: this.temperature,
-                },
-                stream: false,
-            })
-
-            const timeMs = Date.now() - startTime
-            const toolCalls = this.extractToolCalls(response.message)
-
-            return {
-                content: response.message.content,
-                toolCalls,
-                tokens: response.eval_count ?? estimateTokens(response.message.content),
-                timeMs,
-                truncated: false,
-                stopReason: this.determineStopReason(response, toolCalls),
+            if (this.useNativeTools) {
+                return await this.chatWithNativeTools(ollamaMessages, startTime)
             }
+
+            return await this.chatWithXMLTools(ollamaMessages, startTime)
         } catch (error) {
             if (error instanceof Error && error.name === "AbortError") {
                 throw IpuaroError.llm("Request was aborted")
@@ -75,6 +59,131 @@ export class OllamaClient implements ILLMClient {
         }
     }
 
+    /**
+     * Chat using XML-based tool calling (legacy mode).
+     */
+    private async chatWithXMLTools(
+        ollamaMessages: Message[],
+        startTime: number,
+    ): Promise<LLMResponse> {
+        const response = await this.client.chat({
+            model: this.model,
+            messages: ollamaMessages,
+            options: {
+                temperature: this.temperature,
+            },
+            stream: false,
+        })
+
+        const timeMs = Date.now() - startTime
+        const parsed = parseToolCalls(response.message.content)
+
+        return {
+            content: parsed.content,
+            toolCalls: parsed.toolCalls,
+            tokens: response.eval_count ?? estimateTokens(response.message.content),
+            timeMs,
+            truncated: false,
+            stopReason: this.determineStopReason(response, parsed.toolCalls),
+        }
+    }
+
+    /**
+     * Chat using native Ollama tool calling.
+     */
+    private async chatWithNativeTools(
+        ollamaMessages: Message[],
+        startTime: number,
+    ): Promise<LLMResponse> {
+        const nativeTools = getOllamaNativeTools() as Tool[]
+
+        const response = await this.client.chat({
+            model: this.model,
+            messages: ollamaMessages,
+            tools: nativeTools,
+            options: {
+                temperature: this.temperature,
+            },
+            stream: false,
+        })
+
+        const timeMs = Date.now() - startTime
+        let toolCalls = this.parseNativeToolCalls(response.message.tool_calls)
+
+        // Fallback: some models return tool calls as JSON in content
+        if (toolCalls.length === 0 && response.message.content) {
+            toolCalls = this.parseToolCallsFromContent(response.message.content)
+        }
+
+        const content = toolCalls.length > 0 ? "" : response.message.content || ""
+
+        return {
+            content,
+            toolCalls,
+            tokens: response.eval_count ?? estimateTokens(response.message.content || ""),
+            timeMs,
+            truncated: false,
+            stopReason: toolCalls.length > 0 ? "tool_use" : "end",
+        }
+    }
+
+    /**
+     * Parse native Ollama tool calls into ToolCall format.
+     */
+    private parseNativeToolCalls(
+        nativeToolCalls?: { function: { name: string; arguments: Record<string, unknown> } }[],
+    ): ToolCall[] {
+        if (!nativeToolCalls || nativeToolCalls.length === 0) {
+            return []
+        }
+
+        return nativeToolCalls.map((tc, index) =>
+            createToolCall(
+                `native_${String(Date.now())}_${String(index)}`,
+                tc.function.name,
+                tc.function.arguments,
+            ),
+        )
+    }
+
+    /**
+     * Parse tool calls from content (fallback for models that return JSON in content).
+     * Supports format: {"name": "tool_name", "arguments": {...}}
+     */
+    private parseToolCallsFromContent(content: string): ToolCall[] {
+        const toolCalls: ToolCall[] = []
+
+        // Try to parse JSON objects from content
+        const jsonRegex = /\{[\s\S]*?"name"[\s\S]*?"arguments"[\s\S]*?\}/g
+        const matches = content.match(jsonRegex)
+
+        if (!matches) {
+            return toolCalls
+        }
+
+        for (const match of matches) {
+            try {
+                const parsed = JSON.parse(match) as {
+                    name?: string
+                    arguments?: Record<string, unknown>
+                }
+                if (parsed.name && typeof parsed.name === "string") {
+                    toolCalls.push(
+                        createToolCall(
+                            `json_${String(Date.now())}_${String(toolCalls.length)}`,
+                            parsed.name,
+                            parsed.arguments ?? {},
+                        ),
+                    )
+                }
+            } catch {
+                // Invalid JSON, skip
+            }
+        }
+
+        return toolCalls
+    }
+
     /**
      * Count tokens in text.
      * Uses estimation since Ollama doesn't provide a tokenizer endpoint.
@@ -205,69 +314,12 @@ export class OllamaClient implements ILLMClient {
         }
     }
 
-    /**
-     * Convert ToolDef array to Ollama Tool format.
-     */
-    private convertTools(tools: ToolDef[]): Tool[] {
-        return tools.map(
-            (tool): Tool => ({
-                type: "function",
-                function: {
-                    name: tool.name,
-                    description: tool.description,
-                    parameters: {
-                        type: "object",
-                        properties: this.convertParameters(tool.parameters),
-                        required: tool.parameters.filter((p) => p.required).map((p) => p.name),
-                    },
-                },
-            }),
-        )
-    }
-
-    /**
-     * Convert ToolParameter array to JSON Schema properties.
-     */
-    private convertParameters(
-        params: ToolParameter[],
-    ): Record<string, { type: string; description: string; enum?: string[] }> {
-        const properties: Record<string, { type: string; description: string; enum?: string[] }> =
-            {}
-
-        for (const param of params) {
-            properties[param.name] = {
-                type: param.type,
-                description: param.description,
-                ...(param.enum && { enum: param.enum }),
-            }
-        }
-
-        return properties
-    }
-
-    /**
-     * Extract tool calls from Ollama response message.
-     */
-    private extractToolCalls(message: Message): ToolCall[] {
-        if (!message.tool_calls || message.tool_calls.length === 0) {
-            return []
-        }
-
-        return message.tool_calls.map((tc, index) =>
-            createToolCall(
-                `call_${String(Date.now())}_${String(index)}`,
-                tc.function.name,
-                tc.function.arguments,
-            ),
-        )
-    }
-
     /**
      * Determine stop reason from response.
      */
     private determineStopReason(
         response: { done_reason?: string },
-        toolCalls: ToolCall[],
+        toolCalls: { name: string; params: Record<string, unknown> }[],
     ): "end" | "length" | "tool_use" {
         if (toolCalls.length > 0) {
             return "tool_use"

packages/ipuaro/src/infrastructure/llm/ResponseParser.ts

@@ -27,19 +27,103 @@ const TOOL_CALL_REGEX = /<tool_call\s+name\s*=\s*"([^"]+)">([\s\S]*?)<\/tool_cal
 const PARAM_REGEX_NAMED = /<param\s+name\s*=\s*"([^"]+)">([\s\S]*?)<\/param>/gi
 const PARAM_REGEX_ELEMENT = /<([a-z_][a-z0-9_]*)>([\s\S]*?)<\/\1>/gi
 
+/**
+ * CDATA section pattern.
+ * Matches: <![CDATA[...]]>
+ */
+const CDATA_REGEX = /<!\[CDATA\[([\s\S]*?)\]\]>/g
+
+/**
+ * Valid tool names.
+ * Used for validation to catch typos or hallucinations.
+ */
+const VALID_TOOL_NAMES = new Set([
+    "get_lines",
+    "get_function",
+    "get_class",
+    "get_structure",
+    "edit_lines",
+    "create_file",
+    "delete_file",
+    "find_references",
+    "find_definition",
+    "get_dependencies",
+    "get_dependents",
+    "get_complexity",
+    "get_todos",
+    "git_status",
+    "git_diff",
+    "git_commit",
+    "run_command",
+    "run_tests",
+])
+
+/**
+ * Tool name aliases for common LLM typos/variations.
+ * Maps incorrect names to correct tool names.
+ */
+const TOOL_ALIASES: Record<string, string> = {
+    // get_lines aliases
+    get_functions: "get_lines",
+    read_file: "get_lines",
+    read_lines: "get_lines",
+    get_file: "get_lines",
+    read: "get_lines",
+    // get_function aliases
+    getfunction: "get_function",
+    // get_structure aliases
+    list_files: "get_structure",
+    get_files: "get_structure",
+    list_structure: "get_structure",
+    get_project_structure: "get_structure",
+    // get_todos aliases
+    find_todos: "get_todos",
+    list_todos: "get_todos",
+    // find_references aliases
+    get_references: "find_references",
+    // find_definition aliases
+    get_definition: "find_definition",
+    // edit_lines aliases
+    edit_file: "edit_lines",
+    modify_file: "edit_lines",
+    update_file: "edit_lines",
+}
+
+/**
+ * Normalize tool name using aliases.
+ */
+function normalizeToolName(name: string): string {
+    const lowerName = name.toLowerCase()
+    return TOOL_ALIASES[lowerName] ?? name
+}
+
 /**
  * Parse tool calls from LLM response text.
- * Supports XML format: <tool_call name="get_lines"><path>src/index.ts</path></tool_call>
+ * Supports both XML and JSON formats:
+ * - XML: <tool_call name="get_lines"><path>src/index.ts</path></tool_call>
+ * - JSON: {"name": "get_lines", "arguments": {"path": "src/index.ts"}}
+ * Validates tool names and provides helpful error messages.
  */
 export function parseToolCalls(response: string): ParsedResponse {
     const toolCalls: ToolCall[] = []
     const parseErrors: string[] = []
     let content = response
 
-    const matches = [...response.matchAll(TOOL_CALL_REGEX)]
+    // First, try XML format
+    const xmlMatches = [...response.matchAll(TOOL_CALL_REGEX)]
 
-    for (const match of matches) {
-        const [fullMatch, toolName, paramsXml] = match
+    for (const match of xmlMatches) {
+        const [fullMatch, rawToolName, paramsXml] = match
+
+        // Normalize tool name (handle common LLM typos/variations)
+        const toolName = normalizeToolName(rawToolName)
+
+        if (!VALID_TOOL_NAMES.has(toolName)) {
+            parseErrors.push(
+                `Unknown tool "${rawToolName}". Valid tools: ${[...VALID_TOOL_NAMES].join(", ")}`,
+            )
+            continue
+        }
 
         try {
             const params = parseParameters(paramsXml)
@@ -52,7 +136,19 @@ export function parseToolCalls(response: string): ParsedResponse {
             content = content.replace(fullMatch, "")
         } catch (error) {
             const errorMsg = error instanceof Error ? error.message : String(error)
-            parseErrors.push(`Failed to parse tool call "${toolName}": ${errorMsg}`)
+            parseErrors.push(`Failed to parse tool call "${rawToolName}": ${errorMsg}`)
+        }
+    }
+
+    // If no XML tool calls found, try JSON format as fallback
+    if (toolCalls.length === 0) {
+        const jsonResult = parseJsonToolCalls(response)
+        toolCalls.push(...jsonResult.toolCalls)
+        parseErrors.push(...jsonResult.parseErrors)
+
+        // Remove JSON tool calls from content
+        for (const jsonMatch of jsonResult.matchedStrings) {
+            content = content.replace(jsonMatch, "")
         }
     }
 
@@ -66,6 +162,59 @@ export function parseToolCalls(response: string): ParsedResponse {
     }
 }
 
+/**
+ * JSON tool call format pattern.
+ * Matches: {"name": "tool_name", "arguments": {...}}
+ */
+const JSON_TOOL_CALL_REGEX =
+    /\{\s*"name"\s*:\s*"([^"]+)"\s*,\s*"arguments"\s*:\s*(\{[^{}]*(?:\{[^{}]*\}[^{}]*)*\})\s*\}/g
+
+/**
+ * Parse tool calls from JSON format in response.
+ * This is a fallback for LLMs that prefer JSON over XML.
+ */
+function parseJsonToolCalls(response: string): {
+    toolCalls: ToolCall[]
+    parseErrors: string[]
+    matchedStrings: string[]
+} {
+    const toolCalls: ToolCall[] = []
+    const parseErrors: string[] = []
+    const matchedStrings: string[] = []
+
+    const matches = [...response.matchAll(JSON_TOOL_CALL_REGEX)]
+
+    for (const match of matches) {
+        const [fullMatch, rawToolName, argsJson] = match
+        matchedStrings.push(fullMatch)
+
+        // Normalize tool name
+        const toolName = normalizeToolName(rawToolName)
+
+        if (!VALID_TOOL_NAMES.has(toolName)) {
+            parseErrors.push(
+                `Unknown tool "${rawToolName}". Valid tools: ${[...VALID_TOOL_NAMES].join(", ")}`,
+            )
+            continue
+        }
+
+        try {
+            const args = JSON.parse(argsJson) as Record<string, unknown>
+            const toolCall = createToolCall(
+                `json_${String(Date.now())}_${String(toolCalls.length)}`,
+                toolName,
+                args,
+            )
+            toolCalls.push(toolCall)
+        } catch (error) {
+            const errorMsg = error instanceof Error ? error.message : String(error)
+            parseErrors.push(`Failed to parse JSON tool call "${rawToolName}": ${errorMsg}`)
+        }
+    }
+
+    return { toolCalls, parseErrors, matchedStrings }
+}
+
 /**
  * Parse parameters from XML content.
  */
@@ -91,10 +240,16 @@ function parseParameters(xml: string): Record<string, unknown> {
 
 /**
  * Parse a value string to appropriate type.
+ * Supports CDATA sections for multiline content.
  */
 function parseValue(value: string): unknown {
     const trimmed = value.trim()
 
+    const cdataMatches = [...trimmed.matchAll(CDATA_REGEX)]
+    if (cdataMatches.length > 0 && cdataMatches[0][1] !== undefined) {
+        return cdataMatches[0][1]
+    }
+
     if (trimmed === "true") {
         return true
     }

packages/ipuaro/src/infrastructure/llm/prompts.ts

@@ -11,72 +11,129 @@ export interface ProjectStructure {
     directories: string[]
 }
 
+/**
+ * Options for building initial context.
+ */
+export interface BuildContextOptions {
+    includeSignatures?: boolean
+    includeDepsGraph?: boolean
+    includeCircularDeps?: boolean
+    includeHighImpactFiles?: boolean
+    circularDeps?: string[][]
+}
+
 /**
  * System prompt for the ipuaro AI agent.
  */
-export const SYSTEM_PROMPT = `You are ipuaro, a local AI code assistant specialized in helping developers understand and modify their codebase. You operate within a single project directory and have access to powerful tools for reading, searching, analyzing, and editing code.
+export const SYSTEM_PROMPT = `You are ipuaro, a local AI code assistant with tools for reading, searching, analyzing, and editing code.
 
-## Core Principles
+## When to Use Tools
 
-1. **Lazy Loading**: You don't have the full code in context. Use tools to fetch exactly what you need.
-2. **Precision**: Always verify file paths and line numbers before making changes.
-3. **Safety**: Confirm destructive operations. Never execute dangerous commands.
-4. **Efficiency**: Minimize context usage. Request only necessary code sections.
+**Use tools** when the user asks about:
+- Code content (files, functions, classes)
+- Project structure
+- TODOs, complexity, dependencies
+- Git status, diffs, commits
+- Running commands or tests
+
+**Do NOT use tools** for:
+- Greetings ("Hello", "Hi", "Thanks")
+- General questions not about this codebase
+- Clarifying questions back to the user
+
+## MANDATORY: Tools for Code Questions
+
+**CRITICAL:** You have ZERO code in your context. To answer ANY question about code, you MUST first call a tool.
+
+**WRONG:**
+User: "What's in src/index.ts?"
+Assistant: "The file likely contains..." ← WRONG! Call a tool!
+
+**CORRECT:**
+User: "What's in src/index.ts?"
+<tool_call name="get_lines">
+<path>src/index.ts</path>
+</tool_call>
+
+## Tool Call Format
+
+Output this XML format. Do NOT explain before calling - just output the XML:
+
+<tool_call name="TOOL_NAME">
+<param1>value1</param1>
+<param2>value2</param2>
+</tool_call>
+
+## Example Interactions
+
+**Example 1 - Reading a file:**
+User: "Show me the main function in src/app.ts"
+<tool_call name="get_function">
+<path>src/app.ts</path>
+<name>main</name>
+</tool_call>
+
+**Example 2 - Finding TODOs:**
+User: "Are there any TODO comments?"
+<tool_call name="get_todos">
+</tool_call>
+
+**Example 3 - Project structure:**
+User: "What files are in this project?"
+<tool_call name="get_structure">
+<path>.</path>
+</tool_call>
 
 ## Available Tools
 
-### Reading Tools
-- \`get_lines\`: Get specific lines from a file
-- \`get_function\`: Get a function by name
-- \`get_class\`: Get a class by name
-- \`get_structure\`: Get project directory structure
+### Reading
+- get_lines(path, start?, end?) - Read file lines
+- get_function(path, name) - Get function by name
+- get_class(path, name) - Get class by name
+- get_structure(path?, depth?) - List project files
 
-### Editing Tools (require confirmation)
-- \`edit_lines\`: Replace specific lines in a file
-- \`create_file\`: Create a new file
-- \`delete_file\`: Delete a file
+### Analysis
+- get_todos(path?, type?) - Find TODO/FIXME comments
+- get_dependencies(path) - What this file imports
+- get_dependents(path) - What imports this file
+- get_complexity(path?) - Code complexity metrics
+- find_references(symbol) - Find all usages of a symbol
+- find_definition(symbol) - Find where symbol is defined
 
-### Search Tools
-- \`find_references\`: Find all usages of a symbol
-- \`find_definition\`: Find where a symbol is defined
+### Editing (requires confirmation)
+- edit_lines(path, start, end, content) - Modify file lines
+- create_file(path, content) - Create new file
+- delete_file(path) - Delete a file
 
-### Analysis Tools
-- \`get_dependencies\`: Get files this file imports
-- \`get_dependents\`: Get files that import this file
-- \`get_complexity\`: Get complexity metrics
-- \`get_todos\`: Find TODO/FIXME comments
+### Git
+- git_status() - Repository status
+- git_diff(path?, staged?) - Show changes
+- git_commit(message, files?) - Create commit
 
-### Git Tools
-- \`git_status\`: Get repository status
-- \`git_diff\`: Get uncommitted changes
-- \`git_commit\`: Create a commit (requires confirmation)
+### Commands
+- run_command(command, timeout?) - Execute shell command
+- run_tests(path?, filter?) - Run test suite
 
-### Run Tools
-- \`run_command\`: Execute a shell command (security checked)
-- \`run_tests\`: Run the test suite
+## Rules
 
-## Response Guidelines
+1. **ALWAYS call a tool first** when asked about code - you cannot see any files
+2. **Output XML directly** - don't say "I will use..." just output the tool call
+3. **Wait for results** before making conclusions
+4. **Be concise** in your responses
+5. **Verify before editing** - always read code before modifying it
+6. **Stay safe** - never execute destructive commands without user confirmation`
 
-1. **Be concise**: Don't repeat information already in context.
-2. **Show your work**: Explain what tools you're using and why.
-3. **Verify before editing**: Always read the target code before modifying it.
-4. **Handle errors gracefully**: If a tool fails, explain what went wrong and suggest alternatives.
+/**
+ * Tool usage reminder - appended to messages to reinforce tool usage.
+ * This is added as the last system message before LLM call.
+ */
+export const TOOL_REMINDER = `⚠️ REMINDER: To answer this question, you MUST use a tool first.
+Output the <tool_call> XML directly. Do NOT describe what you will do - just call the tool.
 
-## Code Editing Rules
-
-1. Always use \`get_lines\` or \`get_function\` before \`edit_lines\`.
-2. Provide exact line numbers for edits.
-3. For large changes, break into multiple small edits.
-4. After editing, suggest running tests if available.
-
-## Safety Rules
-
-1. Never execute commands that could harm the system.
-2. Never expose sensitive data (API keys, passwords).
-3. Always confirm file deletions and destructive git operations.
-4. Stay within the project directory.
-
-When you need to perform an action, use the appropriate tool. Think step by step about what information you need and which tools will provide it most efficiently.`
+Example - if asked about a file, output:
+<tool_call name="get_lines">
+<path>the/file/path.ts</path>
+</tool_call>`
 
 /**
  * Build initial context from project structure and AST metadata.
@@ -86,12 +143,38 @@ export function buildInitialContext(
     structure: ProjectStructure,
     asts: Map<string, FileAST>,
     metas?: Map<string, FileMeta>,
+    options?: BuildContextOptions,
 ): string {
     const sections: string[] = []
+    const includeSignatures = options?.includeSignatures ?? true
+    const includeDepsGraph = options?.includeDepsGraph ?? true
+    const includeCircularDeps = options?.includeCircularDeps ?? true
+    const includeHighImpactFiles = options?.includeHighImpactFiles ?? true
 
     sections.push(formatProjectHeader(structure))
     sections.push(formatDirectoryTree(structure))
-    sections.push(formatFileOverview(asts, metas))
+    sections.push(formatFileOverview(asts, metas, includeSignatures))
+
+    if (includeDepsGraph && metas && metas.size > 0) {
+        const depsGraph = formatDependencyGraph(metas)
+        if (depsGraph) {
+            sections.push(depsGraph)
+        }
+    }
+
+    if (includeHighImpactFiles && metas && metas.size > 0) {
+        const highImpactSection = formatHighImpactFiles(metas)
+        if (highImpactSection) {
+            sections.push(highImpactSection)
+        }
+    }
+
+    if (includeCircularDeps && options?.circularDeps && options.circularDeps.length > 0) {
+        const circularDepsSection = formatCircularDeps(options.circularDeps)
+        if (circularDepsSection) {
+            sections.push(circularDepsSection)
+        }
+    }
 
     return sections.join("\n\n")
 }
@@ -127,7 +210,11 @@ function formatDirectoryTree(structure: ProjectStructure): string {
 /**
  * Format file overview with AST summaries.
  */
-function formatFileOverview(asts: Map<string, FileAST>, metas?: Map<string, FileMeta>): string {
+function formatFileOverview(
+    asts: Map<string, FileAST>,
+    metas?: Map<string, FileMeta>,
+    includeSignatures = true,
+): string {
     const lines: string[] = ["## Files", ""]
 
     const sortedPaths = [...asts.keys()].sort()
@@ -138,16 +225,183 @@ function formatFileOverview(asts: Map<string, FileAST>, metas?: Map<string, File
         }
 
         const meta = metas?.get(path)
-        lines.push(formatFileSummary(path, ast, meta))
+        lines.push(formatFileSummary(path, ast, meta, includeSignatures))
     }
 
     return lines.join("\n")
 }
 
 /**
- * Format a single file's AST summary.
+ * Format decorators as a prefix string.
+ * Example: "@Get(':id') @Auth() "
  */
-function formatFileSummary(path: string, ast: FileAST, meta?: FileMeta): string {
+function formatDecoratorsPrefix(decorators: string[] | undefined): string {
+    if (!decorators || decorators.length === 0) {
+        return ""
+    }
+    return `${decorators.join(" ")} `
+}
+
+/**
+ * Format a function signature.
+ */
+function formatFunctionSignature(fn: FileAST["functions"][0]): string {
+    const decoratorsPrefix = formatDecoratorsPrefix(fn.decorators)
+    const asyncPrefix = fn.isAsync ? "async " : ""
+    const params = fn.params
+        .map((p) => {
+            const optional = p.optional ? "?" : ""
+            const type = p.type ? `: ${p.type}` : ""
+            return `${p.name}${optional}${type}`
+        })
+        .join(", ")
+    const returnType = fn.returnType ? `: ${fn.returnType}` : ""
+    return `${decoratorsPrefix}${asyncPrefix}${fn.name}(${params})${returnType}`
+}
+
+/**
+ * Format an interface signature with fields.
+ * Example: "interface User extends Base { id: string, name: string, email?: string }"
+ */
+function formatInterfaceSignature(iface: FileAST["interfaces"][0]): string {
+    const extList = iface.extends ?? []
+    const ext = extList.length > 0 ? ` extends ${extList.join(", ")}` : ""
+
+    if (iface.properties.length === 0) {
+        return `interface ${iface.name}${ext}`
+    }
+
+    const fields = iface.properties
+        .map((p) => {
+            const readonly = p.isReadonly ? "readonly " : ""
+            const optional = p.name.endsWith("?") ? "" : ""
+            const type = p.type ? `: ${p.type}` : ""
+            return `${readonly}${p.name}${optional}${type}`
+        })
+        .join(", ")
+
+    return `interface ${iface.name}${ext} { ${fields} }`
+}
+
+/**
+ * Format a type alias signature with definition.
+ * Example: "type UserId = string" or "type Handler = (event: Event) => void"
+ */
+function formatTypeAliasSignature(type: FileAST["typeAliases"][0]): string {
+    if (!type.definition) {
+        return `type ${type.name}`
+    }
+
+    const definition = truncateDefinition(type.definition, 80)
+    return `type ${type.name} = ${definition}`
+}
+
+/**
+ * Format an enum signature with members and values.
+ * Example: "enum Status { Active=1, Inactive=0, Pending=2 }"
+ * Example: "const enum Role { Admin="admin", User="user" }"
+ */
+function formatEnumSignature(enumInfo: FileAST["enums"][0]): string {
+    const constPrefix = enumInfo.isConst ? "const " : ""
+
+    if (enumInfo.members.length === 0) {
+        return `${constPrefix}enum ${enumInfo.name}`
+    }
+
+    const membersStr = enumInfo.members
+        .map((m) => {
+            if (m.value === undefined) {
+                return m.name
+            }
+            const valueStr = typeof m.value === "string" ? `"${m.value}"` : String(m.value)
+            return `${m.name}=${valueStr}`
+        })
+        .join(", ")
+
+    const result = `${constPrefix}enum ${enumInfo.name} { ${membersStr} }`
+
+    if (result.length > 100) {
+        return truncateDefinition(result, 100)
+    }
+
+    return result
+}
+
+/**
+ * Truncate long type definitions for display.
+ */
+function truncateDefinition(definition: string, maxLength: number): string {
+    const normalized = definition.replace(/\s+/g, " ").trim()
+    if (normalized.length <= maxLength) {
+        return normalized
+    }
+    return `${normalized.slice(0, maxLength - 3)}...`
+}
+
+/**
+ * Format a single file's AST summary.
+ * When includeSignatures is true, shows full function signatures.
+ * When false, shows compact format with just names.
+ */
+function formatFileSummary(
+    path: string,
+    ast: FileAST,
+    meta?: FileMeta,
+    includeSignatures = true,
+): string {
+    const flags = formatFileFlags(meta)
+
+    if (!includeSignatures) {
+        return formatFileSummaryCompact(path, ast, flags)
+    }
+
+    const lines: string[] = []
+    lines.push(`### ${path}${flags}`)
+
+    if (ast.functions.length > 0) {
+        for (const fn of ast.functions) {
+            lines.push(`- ${formatFunctionSignature(fn)}`)
+        }
+    }
+
+    if (ast.classes.length > 0) {
+        for (const cls of ast.classes) {
+            const decoratorsPrefix = formatDecoratorsPrefix(cls.decorators)
+            const ext = cls.extends ? ` extends ${cls.extends}` : ""
+            const impl = cls.implements.length > 0 ? ` implements ${cls.implements.join(", ")}` : ""
+            lines.push(`- ${decoratorsPrefix}class ${cls.name}${ext}${impl}`)
+        }
+    }
+
+    if (ast.interfaces.length > 0) {
+        for (const iface of ast.interfaces) {
+            lines.push(`- ${formatInterfaceSignature(iface)}`)
+        }
+    }
+
+    if (ast.typeAliases.length > 0) {
+        for (const type of ast.typeAliases) {
+            lines.push(`- ${formatTypeAliasSignature(type)}`)
+        }
+    }
+
+    if (ast.enums && ast.enums.length > 0) {
+        for (const enumInfo of ast.enums) {
+            lines.push(`- ${formatEnumSignature(enumInfo)}`)
+        }
+    }
+
+    if (lines.length === 1) {
+        return `- ${path}${flags}`
+    }
+
+    return lines.join("\n")
+}
+
+/**
+ * Format file summary in compact mode (just names, no signatures).
+ */
+function formatFileSummaryCompact(path: string, ast: FileAST, flags: string): string {
     const parts: string[] = []
 
     if (ast.functions.length > 0) {
@@ -170,9 +424,12 @@ function formatFileSummary(path: string, ast: FileAST, meta?: FileMeta): string
         parts.push(`type: ${names}`)
     }
 
-    const summary = parts.length > 0 ? ` [${parts.join(" | ")}]` : ""
-    const flags = formatFileFlags(meta)
+    if (ast.enums && ast.enums.length > 0) {
+        const names = ast.enums.map((e) => e.name).join(", ")
+        parts.push(`enum: ${names}`)
+    }
 
+    const summary = parts.length > 0 ? ` [${parts.join(" | ")}]` : ""
     return `- ${path}${summary}${flags}`
 }
 
@@ -201,6 +458,220 @@ function formatFileFlags(meta?: FileMeta): string {
     return flags.length > 0 ? ` (${flags.join(", ")})` : ""
 }
 
+/**
+ * Shorten a file path for display in dependency graph.
+ * Removes common prefixes like "src/" and file extensions.
+ */
+function shortenPath(path: string): string {
+    let short = path
+    if (short.startsWith("src/")) {
+        short = short.slice(4)
+    }
+    // Remove common extensions
+    short = short.replace(/\.(ts|tsx|js|jsx)$/, "")
+    // Remove /index suffix
+    short = short.replace(/\/index$/, "")
+    return short
+}
+
+/**
+ * Format a single dependency graph entry.
+ * Format: "path: → dep1, dep2 ← dependent1, dependent2"
+ */
+function formatDepsEntry(path: string, dependencies: string[], dependents: string[]): string {
+    const parts: string[] = []
+    const shortPath = shortenPath(path)
+
+    if (dependencies.length > 0) {
+        const deps = dependencies.map(shortenPath).join(", ")
+        parts.push(`→ ${deps}`)
+    }
+
+    if (dependents.length > 0) {
+        const deps = dependents.map(shortenPath).join(", ")
+        parts.push(`← ${deps}`)
+    }
+
+    if (parts.length === 0) {
+        return ""
+    }
+
+    return `${shortPath}: ${parts.join(" ")}`
+}
+
+/**
+ * Format dependency graph for all files.
+ * Shows hub files first, then files with dependencies/dependents.
+ *
+ * Format:
+ * ## Dependency Graph
+ * services/user: → types/user, utils/validation ← controllers/user
+ * services/auth: → services/user, utils/jwt ← controllers/auth
+ */
+export function formatDependencyGraph(metas: Map<string, FileMeta>): string | null {
+    if (metas.size === 0) {
+        return null
+    }
+
+    const entries: { path: string; deps: string[]; dependents: string[]; isHub: boolean }[] = []
+
+    for (const [path, meta] of metas) {
+        // Only include files that have connections
+        if (meta.dependencies.length > 0 || meta.dependents.length > 0) {
+            entries.push({
+                path,
+                deps: meta.dependencies,
+                dependents: meta.dependents,
+                isHub: meta.isHub,
+            })
+        }
+    }
+
+    if (entries.length === 0) {
+        return null
+    }
+
+    // Sort: hubs first, then by total connections (desc), then by path
+    entries.sort((a, b) => {
+        if (a.isHub !== b.isHub) {
+            return a.isHub ? -1 : 1
+        }
+        const aTotal = a.deps.length + a.dependents.length
+        const bTotal = b.deps.length + b.dependents.length
+        if (aTotal !== bTotal) {
+            return bTotal - aTotal
+        }
+        return a.path.localeCompare(b.path)
+    })
+
+    const lines: string[] = ["## Dependency Graph", ""]
+
+    for (const entry of entries) {
+        const line = formatDepsEntry(entry.path, entry.deps, entry.dependents)
+        if (line) {
+            lines.push(line)
+        }
+    }
+
+    // Return null if only header (no actual entries)
+    if (lines.length <= 2) {
+        return null
+    }
+
+    return lines.join("\n")
+}
+
+/**
+ * Format circular dependencies for display in context.
+ * Shows warning section with cycle chains.
+ *
+ * Format:
+ * ## ⚠️ Circular Dependencies
+ * - services/user → services/auth → services/user
+ * - utils/a → utils/b → utils/c → utils/a
+ */
+export function formatCircularDeps(cycles: string[][]): string | null {
+    if (!cycles || cycles.length === 0) {
+        return null
+    }
+
+    const lines: string[] = ["## ⚠️ Circular Dependencies", ""]
+
+    for (const cycle of cycles) {
+        if (cycle.length === 0) {
+            continue
+        }
+        const formattedCycle = cycle.map(shortenPath).join(" → ")
+        lines.push(`- ${formattedCycle}`)
+    }
+
+    // Return null if only header (no actual cycles)
+    if (lines.length <= 2) {
+        return null
+    }
+
+    return lines.join("\n")
+}
+
+/**
+ * Format high impact files table for display in context.
+ * Shows files with highest impact scores (most dependents).
+ * Includes both direct and transitive dependent counts.
+ *
+ * Format:
+ * ## High Impact Files
+ * | File | Impact | Direct | Transitive |
+ * |------|--------|--------|------------|
+ * | src/utils/validation.ts | 67% | 12 | 24 |
+ *
+ * @param metas - Map of file paths to their metadata
+ * @param limit - Maximum number of files to show (default: 10)
+ * @param minImpact - Minimum impact score to include (default: 5)
+ */
+export function formatHighImpactFiles(
+    metas: Map<string, FileMeta>,
+    limit = 10,
+    minImpact = 5,
+): string | null {
+    if (metas.size === 0) {
+        return null
+    }
+
+    // Collect files with impact score >= minImpact
+    const impactFiles: {
+        path: string
+        impact: number
+        dependents: number
+        transitive: number
+    }[] = []
+
+    for (const [path, meta] of metas) {
+        if (meta.impactScore >= minImpact) {
+            impactFiles.push({
+                path,
+                impact: meta.impactScore,
+                dependents: meta.dependents.length,
+                transitive: meta.transitiveDepCount,
+            })
+        }
+    }
+
+    if (impactFiles.length === 0) {
+        return null
+    }
+
+    // Sort by transitive count descending, then by impact, then by path
+    impactFiles.sort((a, b) => {
+        if (a.transitive !== b.transitive) {
+            return b.transitive - a.transitive
+        }
+        if (a.impact !== b.impact) {
+            return b.impact - a.impact
+        }
+        return a.path.localeCompare(b.path)
+    })
+
+    // Take top N files
+    const topFiles = impactFiles.slice(0, limit)
+
+    const lines: string[] = [
+        "## High Impact Files",
+        "",
+        "| File | Impact | Direct | Transitive |",
+        "|------|--------|--------|------------|",
+    ]
+
+    for (const file of topFiles) {
+        const shortPath = shortenPath(file.path)
+        const impact = `${String(file.impact)}%`
+        const direct = String(file.dependents)
+        const transitive = String(file.transitive)
+        lines.push(`| ${shortPath} | ${impact} | ${direct} | ${transitive} |`)
+    }
+
+    return lines.join("\n")
+}
+
 /**
  * Format line range for display.
  */

packages/ipuaro/src/infrastructure/llm/toolDefs.ts

@@ -1,4 +1,4 @@
-import type { ToolDef } from "../../domain/services/ILLMClient.js"
+import type { ToolDef } from "../../shared/types/tool-definitions.js"
 
 /**
  * Tool definitions for ipuaro LLM.
@@ -509,3 +509,87 @@ export function getToolsByCategory(category: string): ToolDef[] {
             return []
     }
 }
+
+/*
+ * =============================================================================
+ * Native Ollama Tools Format
+ * =============================================================================
+ */
+
+/**
+ * Ollama native tool definition format.
+ */
+export interface OllamaTool {
+    type: "function"
+    function: {
+        name: string
+        description: string
+        parameters: {
+            type: "object"
+            properties: Record<string, OllamaToolProperty>
+            required: string[]
+        }
+    }
+}
+
+interface OllamaToolProperty {
+    type: string
+    description: string
+    enum?: string[]
+    items?: { type: string }
+}
+
+/**
+ * Convert ToolDef to Ollama native format.
+ */
+function convertToOllamaTool(tool: ToolDef): OllamaTool {
+    const properties: Record<string, OllamaToolProperty> = {}
+    const required: string[] = []
+
+    for (const param of tool.parameters) {
+        const prop: OllamaToolProperty = {
+            type: param.type === "array" ? "array" : param.type,
+            description: param.description,
+        }
+
+        if (param.enum) {
+            prop.enum = param.enum
+        }
+
+        if (param.type === "array") {
+            prop.items = { type: "string" }
+        }
+
+        properties[param.name] = prop
+
+        if (param.required) {
+            required.push(param.name)
+        }
+    }
+
+    return {
+        type: "function",
+        function: {
+            name: tool.name,
+            description: tool.description,
+            parameters: {
+                type: "object",
+                properties,
+                required,
+            },
+        },
+    }
+}
+
+/**
+ * All tools in Ollama native format.
+ * Used when useNativeTools is enabled.
+ */
+export const OLLAMA_NATIVE_TOOLS: OllamaTool[] = ALL_TOOLS.map(convertToOllamaTool)
+
+/**
+ * Get native tool definitions for Ollama.
+ */
+export function getOllamaNativeTools(): OllamaTool[] {
+    return OLLAMA_NATIVE_TOOLS
+}

packages/ipuaro/src/infrastructure/security/PathValidator.ts

@@ -0,0 +1,293 @@
+import * as path from "node:path"
+import { promises as fs } from "node:fs"
+
+/**
+ * Path validation result classification.
+ */
+export type PathValidationStatus = "valid" | "invalid" | "outside_project"
+
+/**
+ * Result of path validation.
+ */
+export interface PathValidationResult {
+    /** Validation status */
+    status: PathValidationStatus
+    /** Reason for the status */
+    reason: string
+    /** Normalized absolute path (only if valid) */
+    absolutePath?: string
+    /** Normalized relative path (only if valid) */
+    relativePath?: string
+}
+
+/**
+ * Options for path validation.
+ */
+export interface PathValidatorOptions {
+    /** Allow paths that don't exist yet (for create operations) */
+    allowNonExistent?: boolean
+    /** Check if path is a directory */
+    requireDirectory?: boolean
+    /** Check if path is a file */
+    requireFile?: boolean
+    /** Follow symlinks when checking existence */
+    followSymlinks?: boolean
+}
+
+/**
+ * Path validator for ensuring file operations stay within project boundaries.
+ * Prevents path traversal attacks and unauthorized file access.
+ */
+export class PathValidator {
+    private readonly projectRoot: string
+
+    constructor(projectRoot: string) {
+        this.projectRoot = path.resolve(projectRoot)
+    }
+
+    /**
+     * Validate a path and return detailed result.
+     * @param inputPath - Path to validate (relative or absolute)
+     * @param options - Validation options
+     */
+    async validate(
+        inputPath: string,
+        options: PathValidatorOptions = {},
+    ): Promise<PathValidationResult> {
+        if (!inputPath || inputPath.trim() === "") {
+            return {
+                status: "invalid",
+                reason: "Path is empty",
+            }
+        }
+
+        const normalizedInput = inputPath.trim()
+
+        if (this.containsTraversalPatterns(normalizedInput)) {
+            return {
+                status: "invalid",
+                reason: "Path contains traversal patterns",
+            }
+        }
+
+        const absolutePath = path.resolve(this.projectRoot, normalizedInput)
+
+        if (!this.isWithinProject(absolutePath)) {
+            return {
+                status: "outside_project",
+                reason: "Path is outside project root",
+            }
+        }
+
+        const relativePath = path.relative(this.projectRoot, absolutePath)
+
+        if (!options.allowNonExistent) {
+            const existsResult = await this.checkExists(absolutePath, options)
+            if (existsResult) {
+                return existsResult
+            }
+        }
+
+        return {
+            status: "valid",
+            reason: "Path is valid",
+            absolutePath,
+            relativePath,
+        }
+    }
+
+    /**
+     * Synchronous validation for simple checks.
+     * Does not check file existence or type.
+     * @param inputPath - Path to validate (relative or absolute)
+     */
+    validateSync(inputPath: string): PathValidationResult {
+        if (!inputPath || inputPath.trim() === "") {
+            return {
+                status: "invalid",
+                reason: "Path is empty",
+            }
+        }
+
+        const normalizedInput = inputPath.trim()
+
+        if (this.containsTraversalPatterns(normalizedInput)) {
+            return {
+                status: "invalid",
+                reason: "Path contains traversal patterns",
+            }
+        }
+
+        const absolutePath = path.resolve(this.projectRoot, normalizedInput)
+
+        if (!this.isWithinProject(absolutePath)) {
+            return {
+                status: "outside_project",
+                reason: "Path is outside project root",
+            }
+        }
+
+        const relativePath = path.relative(this.projectRoot, absolutePath)
+
+        return {
+            status: "valid",
+            reason: "Path is valid",
+            absolutePath,
+            relativePath,
+        }
+    }
+
+    /**
+     * Quick check if path is within project.
+     * @param inputPath - Path to check (relative or absolute)
+     */
+    isWithin(inputPath: string): boolean {
+        if (!inputPath || inputPath.trim() === "") {
+            return false
+        }
+
+        const normalizedInput = inputPath.trim()
+
+        if (this.containsTraversalPatterns(normalizedInput)) {
+            return false
+        }
+
+        const absolutePath = path.resolve(this.projectRoot, normalizedInput)
+        return this.isWithinProject(absolutePath)
+    }
+
+    /**
+     * Resolve a path relative to project root.
+     * Returns null if path would be outside project.
+     * @param inputPath - Path to resolve
+     */
+    resolve(inputPath: string): string | null {
+        const result = this.validateSync(inputPath)
+        return result.status === "valid" ? (result.absolutePath ?? null) : null
+    }
+
+    /**
+     * Resolve a path or throw an error if invalid.
+     * @param inputPath - Path to resolve
+     * @returns Tuple of [absolutePath, relativePath]
+     * @throws Error if path is invalid
+     */
+    resolveOrThrow(inputPath: string): [absolutePath: string, relativePath: string] {
+        const result = this.validateSync(inputPath)
+        if (result.status !== "valid" || result.absolutePath === undefined) {
+            throw new Error(result.reason)
+        }
+        return [result.absolutePath, result.relativePath ?? ""]
+    }
+
+    /**
+     * Get relative path from project root.
+     * Returns null if path would be outside project.
+     * @param inputPath - Path to make relative
+     */
+    relativize(inputPath: string): string | null {
+        const result = this.validateSync(inputPath)
+        return result.status === "valid" ? (result.relativePath ?? null) : null
+    }
+
+    /**
+     * Get the project root path.
+     */
+    getProjectRoot(): string {
+        return this.projectRoot
+    }
+
+    /**
+     * Check if path contains directory traversal patterns.
+     */
+    private containsTraversalPatterns(inputPath: string): boolean {
+        const normalized = inputPath.replace(/\\/g, "/")
+
+        if (normalized.includes("..")) {
+            return true
+        }
+
+        if (normalized.startsWith("~")) {
+            return true
+        }
+
+        return false
+    }
+
+    /**
+     * Check if absolute path is within project root.
+     */
+    private isWithinProject(absolutePath: string): boolean {
+        const normalizedProject = this.projectRoot.replace(/\\/g, "/")
+        const normalizedPath = absolutePath.replace(/\\/g, "/")
+
+        if (normalizedPath === normalizedProject) {
+            return true
+        }
+
+        const projectWithSep = normalizedProject.endsWith("/")
+            ? normalizedProject
+            : `${normalizedProject}/`
+
+        return normalizedPath.startsWith(projectWithSep)
+    }
+
+    /**
+     * Check file existence and type.
+     */
+    private async checkExists(
+        absolutePath: string,
+        options: PathValidatorOptions,
+    ): Promise<PathValidationResult | null> {
+        try {
+            const statFn = options.followSymlinks ? fs.stat : fs.lstat
+            const stats = await statFn(absolutePath)
+
+            if (options.requireDirectory && !stats.isDirectory()) {
+                return {
+                    status: "invalid",
+                    reason: "Path is not a directory",
+                }
+            }
+
+            if (options.requireFile && !stats.isFile()) {
+                return {
+                    status: "invalid",
+                    reason: "Path is not a file",
+                }
+            }
+
+            return null
+        } catch (error) {
+            if ((error as NodeJS.ErrnoException).code === "ENOENT") {
+                return {
+                    status: "invalid",
+                    reason: "Path does not exist",
+                }
+            }
+
+            return {
+                status: "invalid",
+                reason: `Cannot access path: ${(error as Error).message}`,
+            }
+        }
+    }
+}
+
+/**
+ * Create a path validator for a project.
+ * @param projectRoot - Root directory of the project
+ */
+export function createPathValidator(projectRoot: string): PathValidator {
+    return new PathValidator(projectRoot)
+}
+
+/**
+ * Standalone function for quick path validation.
+ * @param inputPath - Path to validate
+ * @param projectRoot - Project root directory
+ */
+export function validatePath(inputPath: string, projectRoot: string): boolean {
+    const validator = new PathValidator(projectRoot)
+    return validator.isWithin(inputPath)
+}

packages/ipuaro/src/infrastructure/security/index.ts

@@ -0,0 +1,9 @@
+// Security module exports
+export {
+    PathValidator,
+    createPathValidator,
+    validatePath,
+    type PathValidationResult,
+    type PathValidationStatus,
+    type PathValidatorOptions,
+} from "./PathValidator.js"

packages/ipuaro/src/infrastructure/tools/edit/CreateFileTool.ts

@@ -8,6 +8,7 @@ import {
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
 import { hashLines } from "../../../shared/utils/hash.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from create_file tool.
@@ -62,17 +63,18 @@ export class CreateFileTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
+        const inputPath = params.path as string
         const content = params.content as string
 
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/edit/DeleteFileTool.ts

@@ -1,11 +1,11 @@
 import { promises as fs } from "node:fs"
-import * as path from "node:path"
 import type { ITool, ToolContext, ToolParameterSchema } from "../../../domain/services/ITool.js"
 import {
     createErrorResult,
     createSuccessResult,
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from delete_file tool.
@@ -49,15 +49,16 @@ export class DeleteFileTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const inputPath = params.path as string
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/edit/EditLinesTool.ts

@@ -1,5 +1,4 @@
 import { promises as fs } from "node:fs"
-import * as path from "node:path"
 import type { ITool, ToolContext, ToolParameterSchema } from "../../../domain/services/ITool.js"
 import { createFileData } from "../../../domain/value-objects/FileData.js"
 import {
@@ -8,6 +7,7 @@ import {
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
 import { hashLines } from "../../../shared/utils/hash.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from edit_lines tool.
@@ -94,19 +94,20 @@ export class EditLinesTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
+        const inputPath = params.path as string
         const startLine = params.start as number
         const endLine = params.end as number
         const newContent = params.content as string
 
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/read/GetClassTool.ts

@@ -1,5 +1,4 @@
 import { promises as fs } from "node:fs"
-import * as path from "node:path"
 import type { ITool, ToolContext, ToolParameterSchema } from "../../../domain/services/ITool.js"
 import type { ClassInfo } from "../../../domain/value-objects/FileAST.js"
 import {
@@ -7,6 +6,7 @@ import {
     createSuccessResult,
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from get_class tool.
@@ -67,16 +67,17 @@ export class GetClassTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
+        const inputPath = params.path as string
         const className = params.name as string
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/read/GetFunctionTool.ts

@@ -1,5 +1,4 @@
 import { promises as fs } from "node:fs"
-import * as path from "node:path"
 import type { ITool, ToolContext, ToolParameterSchema } from "../../../domain/services/ITool.js"
 import type { FunctionInfo } from "../../../domain/value-objects/FileAST.js"
 import {
@@ -7,6 +6,7 @@ import {
     createSuccessResult,
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from get_function tool.
@@ -65,16 +65,17 @@ export class GetFunctionTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
+        const inputPath = params.path as string
         const functionName = params.name as string
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/read/GetLinesTool.ts

@@ -1,11 +1,11 @@
 import { promises as fs } from "node:fs"
-import * as path from "node:path"
 import type { ITool, ToolContext, ToolParameterSchema } from "../../../domain/services/ITool.js"
 import {
     createErrorResult,
     createSuccessResult,
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Result data from get_lines tool.
@@ -84,15 +84,16 @@ export class GetLinesTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = params.path as string
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const inputPath = params.path as string
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/read/GetStructureTool.ts

@@ -7,6 +7,7 @@ import {
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
 import { DEFAULT_IGNORE_PATTERNS } from "../../../domain/constants/index.js"
+import { PathValidator } from "../../security/PathValidator.js"
 
 /**
  * Tree node representing a file or directory.
@@ -89,16 +90,17 @@ export class GetStructureTool implements ITool {
         const startTime = Date.now()
         const callId = `${this.name}-${String(startTime)}`
 
-        const relativePath = (params.path as string | undefined) ?? ""
+        const inputPath = (params.path as string | undefined) ?? "."
         const maxDepth = params.depth as number | undefined
-        const absolutePath = path.resolve(ctx.projectRoot, relativePath)
+        const pathValidator = new PathValidator(ctx.projectRoot)
 
-        if (!absolutePath.startsWith(ctx.projectRoot)) {
-            return createErrorResult(
-                callId,
-                "Path must be within project root",
-                Date.now() - startTime,
-            )
+        let absolutePath: string
+        let relativePath: string
+        try {
+            ;[absolutePath, relativePath] = pathValidator.resolveOrThrow(inputPath)
+        } catch (error) {
+            const message = error instanceof Error ? error.message : String(error)
+            return createErrorResult(callId, message, Date.now() - startTime)
         }
 
         try {

packages/ipuaro/src/infrastructure/tools/registry.ts

@@ -16,12 +16,7 @@ export class ToolRegistry implements IToolRegistry {
      */
     register(tool: ITool): void {
         if (this.tools.has(tool.name)) {
-            throw new IpuaroError(
-                "validation",
-                `Tool "${tool.name}" is already registered`,
-                true,
-                "Use a different tool name or unregister the existing tool first",
-            )
+            throw IpuaroError.validation(`Tool "${tool.name}" is already registered`)
         }
         this.tools.set(tool.name, tool)
     }

packages/ipuaro/src/infrastructure/tools/run/RunCommandTool.ts

@@ -6,6 +6,7 @@ import {
     createSuccessResult,
     type ToolResult,
 } from "../../../domain/value-objects/ToolResult.js"
+import type { CommandsConfig } from "../../../shared/constants/config.js"
 import { CommandSecurity } from "./CommandSecurity.js"
 
 const execAsync = promisify(exec)
@@ -60,7 +61,7 @@ export class RunCommandTool implements ITool {
         {
             name: "timeout",
             type: "number",
-            description: "Timeout in milliseconds (default: 30000)",
+            description: "Timeout in milliseconds (default: from config or 30000, max: 600000)",
             required: false,
         },
     ]
@@ -69,10 +70,12 @@ export class RunCommandTool implements ITool {
 
     private readonly security: CommandSecurity
     private readonly execFn: typeof execAsync
+    private readonly configTimeout: number | null
 
-    constructor(security?: CommandSecurity, execFn?: typeof execAsync) {
+    constructor(security?: CommandSecurity, execFn?: typeof execAsync, config?: CommandsConfig) {
         this.security = security ?? new CommandSecurity()
         this.execFn = execFn ?? execAsync
+        this.configTimeout = config?.timeout ?? null
     }
 
     validateParams(params: Record<string, unknown>): string | null {
@@ -104,7 +107,7 @@ export class RunCommandTool implements ITool {
         const callId = `${this.name}-${String(startTime)}`
 
         const command = params.command as string
-        const timeout = (params.timeout as number) ?? DEFAULT_TIMEOUT
+        const timeout = (params.timeout as number) ?? this.configTimeout ?? DEFAULT_TIMEOUT
 
         const securityCheck = this.security.check(command)
 

packages/ipuaro/src/shared/constants/config.ts

@@ -20,6 +20,7 @@ export const LLMConfigSchema = z.object({
     temperature: z.number().min(0).max(2).default(0.1),
     host: z.string().default("http://localhost:11434"),
     timeout: z.number().int().positive().default(120_000),
+    useNativeTools: z.boolean().default(false),
 })
 
 /**
@@ -76,6 +77,64 @@ export const UndoConfigSchema = z.object({
  */
 export const EditConfigSchema = z.object({
     autoApply: z.boolean().default(false),
+    syntaxHighlight: z.boolean().default(true),
+})
+
+/**
+ * Input configuration schema.
+ */
+export const InputConfigSchema = z.object({
+    multiline: z.union([z.boolean(), z.literal("auto")]).default(false),
+})
+
+/**
+ * Display configuration schema.
+ */
+export const DisplayConfigSchema = z.object({
+    showStats: z.boolean().default(true),
+    showToolCalls: z.boolean().default(true),
+    theme: z.enum(["dark", "light"]).default("dark"),
+    bellOnComplete: z.boolean().default(false),
+    progressBar: z.boolean().default(true),
+})
+
+/**
+ * Session configuration schema.
+ */
+export const SessionConfigSchema = z.object({
+    persistIndefinitely: z.boolean().default(true),
+    maxHistoryMessages: z.number().int().positive().default(100),
+    saveInputHistory: z.boolean().default(true),
+})
+
+/**
+ * Context configuration schema.
+ */
+export const ContextConfigSchema = z.object({
+    systemPromptTokens: z.number().int().positive().default(2000),
+    maxContextUsage: z.number().min(0).max(1).default(0.8),
+    autoCompressAt: z.number().min(0).max(1).default(0.8),
+    compressionMethod: z.enum(["llm-summary", "truncate"]).default("llm-summary"),
+    includeSignatures: z.boolean().default(true),
+    includeDepsGraph: z.boolean().default(true),
+    includeCircularDeps: z.boolean().default(true),
+    includeHighImpactFiles: z.boolean().default(true),
+})
+
+/**
+ * Autocomplete configuration schema.
+ */
+export const AutocompleteConfigSchema = z.object({
+    enabled: z.boolean().default(true),
+    source: z.enum(["redis-index", "filesystem", "both"]).default("redis-index"),
+    maxSuggestions: z.number().int().positive().default(10),
+})
+
+/**
+ * Commands configuration schema.
+ */
+export const CommandsConfigSchema = z.object({
+    timeout: z.number().int().positive().nullable().default(null),
 })
 
 /**
@@ -88,6 +147,12 @@ export const ConfigSchema = z.object({
     watchdog: WatchdogConfigSchema.default({}),
     undo: UndoConfigSchema.default({}),
     edit: EditConfigSchema.default({}),
+    input: InputConfigSchema.default({}),
+    display: DisplayConfigSchema.default({}),
+    session: SessionConfigSchema.default({}),
+    context: ContextConfigSchema.default({}),
+    autocomplete: AutocompleteConfigSchema.default({}),
+    commands: CommandsConfigSchema.default({}),
 })
 
 /**
@@ -100,6 +165,12 @@ export type ProjectConfig = z.infer<typeof ProjectConfigSchema>
 export type WatchdogConfig = z.infer<typeof WatchdogConfigSchema>
 export type UndoConfig = z.infer<typeof UndoConfigSchema>
 export type EditConfig = z.infer<typeof EditConfigSchema>
+export type InputConfig = z.infer<typeof InputConfigSchema>
+export type DisplayConfig = z.infer<typeof DisplayConfigSchema>
+export type SessionConfig = z.infer<typeof SessionConfigSchema>
+export type ContextConfig = z.infer<typeof ContextConfigSchema>
+export type AutocompleteConfig = z.infer<typeof AutocompleteConfigSchema>
+export type CommandsConfig = z.infer<typeof CommandsConfigSchema>
 
 /**
  * Default configuration.

packages/ipuaro/src/shared/errors/ErrorHandler.ts

@@ -0,0 +1,295 @@
+/**
+ * ErrorHandler service for handling errors with user interaction.
+ * Implements the error handling matrix from ROADMAP.md.
+ */
+
+import { ERROR_MATRIX, type ErrorOption, type ErrorType, IpuaroError } from "./IpuaroError.js"
+
+/**
+ * Result of error handling.
+ */
+export interface ErrorHandlingResult {
+    action: ErrorOption
+    shouldContinue: boolean
+    retryCount?: number
+}
+
+/**
+ * Callback for requesting user choice on error.
+ */
+export type ErrorChoiceCallback = (
+    error: IpuaroError,
+    availableOptions: ErrorOption[],
+    defaultOption: ErrorOption,
+) => Promise<ErrorOption>
+
+/**
+ * Options for ErrorHandler.
+ */
+export interface ErrorHandlerOptions {
+    maxRetries?: number
+    autoSkipParseErrors?: boolean
+    autoRetryLLMErrors?: boolean
+    onError?: ErrorChoiceCallback
+}
+
+const DEFAULT_MAX_RETRIES = 3
+
+/**
+ * Error handler service with matrix-based logic.
+ */
+export class ErrorHandler {
+    private readonly maxRetries: number
+    private readonly autoSkipParseErrors: boolean
+    private readonly autoRetryLLMErrors: boolean
+    private readonly onError?: ErrorChoiceCallback
+
+    private readonly retryCounters = new Map<string, number>()
+
+    constructor(options: ErrorHandlerOptions = {}) {
+        this.maxRetries = options.maxRetries ?? DEFAULT_MAX_RETRIES
+        this.autoSkipParseErrors = options.autoSkipParseErrors ?? true
+        this.autoRetryLLMErrors = options.autoRetryLLMErrors ?? false
+        this.onError = options.onError
+    }
+
+    /**
+     * Handle an error and determine the action to take.
+     */
+    async handle(error: IpuaroError, contextKey?: string): Promise<ErrorHandlingResult> {
+        const key = contextKey ?? error.message
+        const currentRetries = this.retryCounters.get(key) ?? 0
+
+        if (this.shouldAutoHandle(error)) {
+            const autoAction = this.getAutoAction(error, currentRetries)
+            if (autoAction) {
+                return this.createResult(autoAction, key, currentRetries)
+            }
+        }
+
+        if (!error.recoverable) {
+            return {
+                action: "abort",
+                shouldContinue: false,
+            }
+        }
+
+        if (this.onError) {
+            const choice = await this.onError(error, error.options, error.defaultOption)
+            return this.createResult(choice, key, currentRetries)
+        }
+
+        return this.createResult(error.defaultOption, key, currentRetries)
+    }
+
+    /**
+     * Handle an error synchronously with default behavior.
+     */
+    handleSync(error: IpuaroError, contextKey?: string): ErrorHandlingResult {
+        const key = contextKey ?? error.message
+        const currentRetries = this.retryCounters.get(key) ?? 0
+
+        if (this.shouldAutoHandle(error)) {
+            const autoAction = this.getAutoAction(error, currentRetries)
+            if (autoAction) {
+                return this.createResult(autoAction, key, currentRetries)
+            }
+        }
+
+        if (!error.recoverable) {
+            return {
+                action: "abort",
+                shouldContinue: false,
+            }
+        }
+
+        return this.createResult(error.defaultOption, key, currentRetries)
+    }
+
+    /**
+     * Reset retry counters.
+     */
+    resetRetries(contextKey?: string): void {
+        if (contextKey) {
+            this.retryCounters.delete(contextKey)
+        } else {
+            this.retryCounters.clear()
+        }
+    }
+
+    /**
+     * Get retry count for a context.
+     */
+    getRetryCount(contextKey: string): number {
+        return this.retryCounters.get(contextKey) ?? 0
+    }
+
+    /**
+     * Check if max retries exceeded for a context.
+     */
+    isMaxRetriesExceeded(contextKey: string): boolean {
+        return this.getRetryCount(contextKey) >= this.maxRetries
+    }
+
+    /**
+     * Wrap a function with error handling.
+     */
+    async wrap<T>(
+        fn: () => Promise<T>,
+        errorType: ErrorType,
+        contextKey?: string,
+    ): Promise<{ success: true; data: T } | { success: false; result: ErrorHandlingResult }> {
+        try {
+            const data = await fn()
+            if (contextKey) {
+                this.resetRetries(contextKey)
+            }
+            return { success: true, data }
+        } catch (err) {
+            const error =
+                err instanceof IpuaroError
+                    ? err
+                    : new IpuaroError(errorType, err instanceof Error ? err.message : String(err))
+
+            const result = await this.handle(error, contextKey)
+            return { success: false, result }
+        }
+    }
+
+    /**
+     * Wrap a function with retry logic.
+     */
+    async withRetry<T>(fn: () => Promise<T>, errorType: ErrorType, contextKey: string): Promise<T> {
+        const key = contextKey
+
+        while (!this.isMaxRetriesExceeded(key)) {
+            try {
+                const result = await fn()
+                this.resetRetries(key)
+                return result
+            } catch (err) {
+                const error =
+                    err instanceof IpuaroError
+                        ? err
+                        : new IpuaroError(
+                              errorType,
+                              err instanceof Error ? err.message : String(err),
+                          )
+
+                const handlingResult = await this.handle(error, key)
+
+                if (handlingResult.action !== "retry" || !handlingResult.shouldContinue) {
+                    throw error
+                }
+            }
+        }
+
+        throw new IpuaroError(
+            errorType,
+            `Max retries (${String(this.maxRetries)}) exceeded for: ${key}`,
+        )
+    }
+
+    private shouldAutoHandle(error: IpuaroError): boolean {
+        if (error.type === "parse" && this.autoSkipParseErrors) {
+            return true
+        }
+        if ((error.type === "llm" || error.type === "timeout") && this.autoRetryLLMErrors) {
+            return true
+        }
+        return false
+    }
+
+    private getAutoAction(error: IpuaroError, currentRetries: number): ErrorOption | null {
+        if (error.type === "parse" && this.autoSkipParseErrors) {
+            return "skip"
+        }
+
+        if ((error.type === "llm" || error.type === "timeout") && this.autoRetryLLMErrors) {
+            if (currentRetries < this.maxRetries) {
+                return "retry"
+            }
+            return "abort"
+        }
+
+        return null
+    }
+
+    private createResult(
+        action: ErrorOption,
+        key: string,
+        currentRetries: number,
+    ): ErrorHandlingResult {
+        if (action === "retry") {
+            this.retryCounters.set(key, currentRetries + 1)
+            const newRetryCount = currentRetries + 1
+
+            if (newRetryCount > this.maxRetries) {
+                return {
+                    action: "abort",
+                    shouldContinue: false,
+                    retryCount: newRetryCount,
+                }
+            }
+
+            return {
+                action: "retry",
+                shouldContinue: true,
+                retryCount: newRetryCount,
+            }
+        }
+
+        this.retryCounters.delete(key)
+
+        return {
+            action,
+            shouldContinue: action === "skip" || action === "confirm" || action === "regenerate",
+            retryCount: currentRetries,
+        }
+    }
+}
+
+/**
+ * Get available options for an error type.
+ */
+export function getErrorOptions(errorType: ErrorType): ErrorOption[] {
+    return ERROR_MATRIX[errorType].options
+}
+
+/**
+ * Get default option for an error type.
+ */
+export function getDefaultErrorOption(errorType: ErrorType): ErrorOption {
+    return ERROR_MATRIX[errorType].defaultOption
+}
+
+/**
+ * Check if an error type is recoverable by default.
+ */
+export function isRecoverableError(errorType: ErrorType): boolean {
+    return ERROR_MATRIX[errorType].recoverable
+}
+
+/**
+ * Convert any error to IpuaroError.
+ */
+export function toIpuaroError(error: unknown, defaultType: ErrorType = "unknown"): IpuaroError {
+    if (error instanceof IpuaroError) {
+        return error
+    }
+
+    if (error instanceof Error) {
+        return new IpuaroError(defaultType, error.message, {
+            context: { originalError: error.name },
+        })
+    }
+
+    return new IpuaroError(defaultType, String(error))
+}
+
+/**
+ * Create a default ErrorHandler instance.
+ */
+export function createErrorHandler(options?: ErrorHandlerOptions): ErrorHandler {
+    return new ErrorHandler(options)
+}

packages/ipuaro/src/shared/errors/IpuaroError.ts

@@ -12,6 +12,72 @@ export type ErrorType =
     | "timeout"
     | "unknown"
 
+/**
+ * Available options for error recovery.
+ */
+export type ErrorOption = "retry" | "skip" | "abort" | "confirm" | "regenerate"
+
+/**
+ * Error metadata with available options.
+ */
+export interface ErrorMeta {
+    type: ErrorType
+    recoverable: boolean
+    options: ErrorOption[]
+    defaultOption: ErrorOption
+}
+
+/**
+ * Error handling matrix - defines behavior for each error type.
+ */
+export const ERROR_MATRIX: Record<ErrorType, Omit<ErrorMeta, "type">> = {
+    redis: {
+        recoverable: false,
+        options: ["retry", "abort"],
+        defaultOption: "abort",
+    },
+    parse: {
+        recoverable: true,
+        options: ["skip", "abort"],
+        defaultOption: "skip",
+    },
+    llm: {
+        recoverable: true,
+        options: ["retry", "skip", "abort"],
+        defaultOption: "retry",
+    },
+    file: {
+        recoverable: true,
+        options: ["skip", "abort"],
+        defaultOption: "skip",
+    },
+    command: {
+        recoverable: true,
+        options: ["confirm", "skip", "abort"],
+        defaultOption: "confirm",
+    },
+    conflict: {
+        recoverable: true,
+        options: ["skip", "regenerate", "abort"],
+        defaultOption: "skip",
+    },
+    validation: {
+        recoverable: true,
+        options: ["skip", "abort"],
+        defaultOption: "skip",
+    },
+    timeout: {
+        recoverable: true,
+        options: ["retry", "skip", "abort"],
+        defaultOption: "retry",
+    },
+    unknown: {
+        recoverable: false,
+        options: ["abort"],
+        defaultOption: "abort",
+    },
+}
+
 /**
  * Base error class for ipuaro.
  */
@@ -19,60 +85,142 @@ export class IpuaroError extends Error {
     readonly type: ErrorType
     readonly recoverable: boolean
     readonly suggestion?: string
+    readonly options: ErrorOption[]
+    readonly defaultOption: ErrorOption
+    readonly context?: Record<string, unknown>
 
-    constructor(type: ErrorType, message: string, recoverable = true, suggestion?: string) {
+    constructor(
+        type: ErrorType,
+        message: string,
+        options?: {
+            recoverable?: boolean
+            suggestion?: string
+            context?: Record<string, unknown>
+        },
+    ) {
         super(message)
         this.name = "IpuaroError"
         this.type = type
-        this.recoverable = recoverable
-        this.suggestion = suggestion
+
+        const meta = ERROR_MATRIX[type]
+        this.recoverable = options?.recoverable ?? meta.recoverable
+        this.options = meta.options
+        this.defaultOption = meta.defaultOption
+        this.suggestion = options?.suggestion
+        this.context = options?.context
     }
 
-    static redis(message: string): IpuaroError {
-        return new IpuaroError(
-            "redis",
-            message,
-            false,
-            "Please ensure Redis is running: redis-server",
-        )
+    /**
+     * Get error metadata.
+     */
+    getMeta(): ErrorMeta {
+        return {
+            type: this.type,
+            recoverable: this.recoverable,
+            options: this.options,
+            defaultOption: this.defaultOption,
+        }
+    }
+
+    /**
+     * Check if an option is available for this error.
+     */
+    hasOption(option: ErrorOption): boolean {
+        return this.options.includes(option)
+    }
+
+    /**
+     * Create a formatted error message with suggestion.
+     */
+    toDisplayString(): string {
+        let result = `[${this.type}] ${this.message}`
+        if (this.suggestion) {
+            result += `\n  Suggestion: ${this.suggestion}`
+        }
+        return result
+    }
+
+    static redis(message: string, context?: Record<string, unknown>): IpuaroError {
+        return new IpuaroError("redis", message, {
+            suggestion: "Please ensure Redis is running: redis-server",
+            context,
+        })
     }
 
     static parse(message: string, filePath?: string): IpuaroError {
         const msg = filePath ? `${message} in ${filePath}` : message
-        return new IpuaroError("parse", msg, true, "File will be skipped")
+        return new IpuaroError("parse", msg, {
+            suggestion: "File will be skipped during indexing",
+            context: filePath ? { filePath } : undefined,
+        })
     }
 
-    static llm(message: string): IpuaroError {
-        return new IpuaroError(
-            "llm",
-            message,
-            true,
-            "Please ensure Ollama is running and model is available",
-        )
+    static llm(message: string, context?: Record<string, unknown>): IpuaroError {
+        return new IpuaroError("llm", message, {
+            suggestion: "Please ensure Ollama is running and model is available",
+            context,
+        })
     }
 
-    static file(message: string): IpuaroError {
-        return new IpuaroError("file", message, true)
+    static llmTimeout(message: string): IpuaroError {
+        return new IpuaroError("timeout", message, {
+            suggestion: "The LLM request timed out. Try again or check Ollama status.",
+        })
     }
 
-    static command(message: string): IpuaroError {
-        return new IpuaroError("command", message, true)
+    static file(message: string, filePath?: string): IpuaroError {
+        return new IpuaroError("file", message, {
+            suggestion: "Check if the file exists and you have permission to access it",
+            context: filePath ? { filePath } : undefined,
+        })
     }
 
-    static conflict(message: string): IpuaroError {
-        return new IpuaroError(
-            "conflict",
-            message,
-            true,
-            "File was modified externally. Regenerate or skip.",
-        )
+    static fileNotFound(filePath: string): IpuaroError {
+        return new IpuaroError("file", `File not found: ${filePath}`, {
+            suggestion: "Check the file path and try again",
+            context: { filePath },
+        })
     }
 
-    static validation(message: string): IpuaroError {
-        return new IpuaroError("validation", message, true)
+    static command(message: string, command?: string): IpuaroError {
+        return new IpuaroError("command", message, {
+            suggestion: "Command requires confirmation or is not in whitelist",
+            context: command ? { command } : undefined,
+        })
     }
 
-    static timeout(message: string): IpuaroError {
-        return new IpuaroError("timeout", message, true, "Try again or increase timeout")
+    static commandBlacklisted(command: string): IpuaroError {
+        return new IpuaroError("command", `Command is blacklisted: ${command}`, {
+            recoverable: false,
+            suggestion: "This command is not allowed for security reasons",
+            context: { command },
+        })
+    }
+
+    static conflict(message: string, filePath?: string): IpuaroError {
+        return new IpuaroError("conflict", message, {
+            suggestion: "File was modified externally. Regenerate or skip the change.",
+            context: filePath ? { filePath } : undefined,
+        })
+    }
+
+    static validation(message: string, field?: string): IpuaroError {
+        return new IpuaroError("validation", message, {
+            suggestion: "Please check the input and try again",
+            context: field ? { field } : undefined,
+        })
+    }
+
+    static timeout(message: string, timeoutMs?: number): IpuaroError {
+        return new IpuaroError("timeout", message, {
+            suggestion: "Try again or increase the timeout value",
+            context: timeoutMs ? { timeoutMs } : undefined,
+        })
+    }
+
+    static unknown(message: string, originalError?: Error): IpuaroError {
+        return new IpuaroError("unknown", message, {
+            context: originalError ? { originalError: originalError.message } : undefined,
+        })
     }
 }

packages/ipuaro/src/shared/errors/index.ts

@@ -1,2 +1,3 @@
 // Shared errors
 export * from "./IpuaroError.js"
+export * from "./ErrorHandler.js"

packages/ipuaro/src/shared/types/index.ts

@@ -19,9 +19,16 @@ export type ConfirmChoice = "apply" | "cancel" | "edit"
 
 /**
  * User choice for errors.
+ * @deprecated Use ErrorOption from shared/errors instead
  */
 export type ErrorChoice = "retry" | "skip" | "abort"
 
+// Re-export ErrorOption for convenience
+export type { ErrorOption } from "../errors/IpuaroError.js"
+
+// Re-export tool definition types
+export type { ToolDef, ToolParameter } from "./tool-definitions.js"
+
 /**
  * Project structure node.
  */

packages/ipuaro/src/shared/types/tool-definitions.ts

@@ -0,0 +1,21 @@
+/**
+ * Tool parameter definition for LLM prompts.
+ * Used to describe tools in system prompts.
+ */
+export interface ToolParameter {
+    name: string
+    type: "string" | "number" | "boolean" | "array" | "object"
+    description: string
+    required: boolean
+    enum?: string[]
+}
+
+/**
+ * Tool definition for LLM prompts.
+ * Used to describe available tools in the system prompt.
+ */
+export interface ToolDef {
+    name: string
+    description: string
+    parameters: ToolParameter[]
+}

packages/ipuaro/src/tui/App.tsx

@@ -9,12 +9,16 @@ import type { ILLMClient } from "../domain/services/ILLMClient.js"
 import type { ISessionStorage } from "../domain/services/ISessionStorage.js"
 import type { IStorage } from "../domain/services/IStorage.js"
 import type { DiffInfo } from "../domain/services/ITool.js"
-import type { ErrorChoice } from "../shared/types/index.js"
+import type { ErrorOption } from "../shared/errors/IpuaroError.js"
+import type { Config } from "../shared/constants/config.js"
 import type { IToolRegistry } from "../application/interfaces/IToolRegistry.js"
+import type { ConfirmationResult } from "../application/use-cases/ExecuteTool.js"
 import type { ProjectStructure } from "../infrastructure/llm/prompts.js"
-import { Chat, Input, StatusBar } from "./components/index.js"
-import { useHotkeys, useSession } from "./hooks/index.js"
+import { Chat, ConfirmDialog, Input, StatusBar } from "./components/index.js"
+import { type CommandResult, useCommands, useHotkeys, useSession } from "./hooks/index.js"
 import type { AppProps, BranchInfo } from "./types.js"
+import type { ConfirmChoice } from "../shared/types/index.js"
+import { ringBell } from "./utils/bell.js"
 
 export interface AppDependencies {
     storage: IStorage
@@ -22,11 +26,18 @@ export interface AppDependencies {
     llm: ILLMClient
     tools: IToolRegistry
     projectStructure?: ProjectStructure
+    config?: Config
 }
 
 export interface ExtendedAppProps extends AppProps {
     deps: AppDependencies
     onExit?: () => void
+    multiline?: boolean | "auto"
+    syntaxHighlight?: boolean
+    theme?: "dark" | "light"
+    showStats?: boolean
+    showToolCalls?: boolean
+    bellOnComplete?: boolean
 }
 
 function LoadingScreen(): React.JSX.Element {
@@ -48,42 +59,110 @@ function ErrorScreen({ error }: { error: Error }): React.JSX.Element {
     )
 }
 
-async function handleConfirmationDefault(_message: string, _diff?: DiffInfo): Promise<boolean> {
-    return Promise.resolve(true)
+async function handleErrorDefault(_error: Error): Promise<ErrorOption> {
+    return Promise.resolve("skip")
 }
 
-async function handleErrorDefault(_error: Error): Promise<ErrorChoice> {
-    return Promise.resolve("skip")
+interface PendingConfirmation {
+    message: string
+    diff?: DiffInfo
+    resolve: (result: boolean | ConfirmationResult) => void
 }
 
 export function App({
     projectPath,
-    autoApply = false,
+    autoApply: initialAutoApply = false,
     deps,
     onExit,
+    multiline = false,
+    syntaxHighlight = true,
+    theme = "dark",
+    showStats = true,
+    showToolCalls = true,
+    bellOnComplete = false,
 }: ExtendedAppProps): React.JSX.Element {
     const { exit } = useApp()
 
     const [branch] = useState<BranchInfo>({ name: "main", isDetached: false })
     const [sessionTime, setSessionTime] = useState("0m")
+    const [autoApply, setAutoApply] = useState(initialAutoApply)
+    const [commandResult, setCommandResult] = useState<CommandResult | null>(null)
+    const [pendingConfirmation, setPendingConfirmation] = useState<PendingConfirmation | null>(null)
 
     const projectName = projectPath.split("/").pop() ?? "unknown"
 
-    const { session, messages, status, isLoading, error, sendMessage, undo, abort } = useSession(
+    const handleConfirmation = useCallback(
+        async (message: string, diff?: DiffInfo): Promise<boolean | ConfirmationResult> => {
+            return new Promise((resolve) => {
+                setPendingConfirmation({ message, diff, resolve })
+            })
+        },
+        [],
+    )
+
+    const handleConfirmSelect = useCallback(
+        (choice: ConfirmChoice, editedContent?: string[]) => {
+            if (!pendingConfirmation) {
+                return
+            }
+
+            if (choice === "apply") {
+                if (editedContent) {
+                    pendingConfirmation.resolve({ confirmed: true, editedContent })
+                } else {
+                    pendingConfirmation.resolve(true)
+                }
+            } else {
+                pendingConfirmation.resolve(false)
+            }
+
+            setPendingConfirmation(null)
+        },
+        [pendingConfirmation],
+    )
+
+    const { session, messages, status, isLoading, error, sendMessage, undo, clearHistory, abort } =
+        useSession(
+            {
+                storage: deps.storage,
+                sessionStorage: deps.sessionStorage,
+                llm: deps.llm,
+                tools: deps.tools,
+                projectRoot: projectPath,
+                projectName,
+                projectStructure: deps.projectStructure,
+                config: deps.config,
+            },
+            {
+                autoApply,
+                onConfirmation: handleConfirmation,
+                onError: handleErrorDefault,
+            },
+        )
+
+    const reindex = useCallback(async (): Promise<void> => {
+        const { IndexProject } = await import("../application/use-cases/IndexProject.js")
+        const indexProject = new IndexProject(deps.storage, projectPath)
+        await indexProject.execute(projectPath)
+    }, [deps.storage, projectPath])
+
+    const { executeCommand, isCommand } = useCommands(
         {
-            storage: deps.storage,
+            session,
             sessionStorage: deps.sessionStorage,
+            storage: deps.storage,
             llm: deps.llm,
             tools: deps.tools,
             projectRoot: projectPath,
             projectName,
-            projectStructure: deps.projectStructure,
         },
         {
-            autoApply,
-            onConfirmation: handleConfirmationDefault,
-            onError: handleErrorDefault,
+            clearHistory,
+            undo,
+            setAutoApply,
+            reindex,
         },
+        { autoApply },
     )
 
     const handleExit = useCallback((): void => {
@@ -126,14 +205,27 @@ export function App({
         }
     }, [session])
 
+    useEffect(() => {
+        if (bellOnComplete && status === "ready") {
+            ringBell()
+        }
+    }, [bellOnComplete, status])
+
     const handleSubmit = useCallback(
         (text: string): void => {
-            if (text.startsWith("/")) {
+            if (isCommand(text)) {
+                void executeCommand(text).then((result) => {
+                    setCommandResult(result)
+                    // Auto-clear command result after 5 seconds
+                    setTimeout(() => {
+                        setCommandResult(null)
+                    }, 5000)
+                })
                 return
             }
             void sendMessage(text)
         },
-        [sendMessage],
+        [sendMessage, isCommand, executeCommand],
     )
 
     if (isLoading) {
@@ -144,7 +236,7 @@ export function App({
         return <ErrorScreen error={error} />
     }
 
-    const isInputDisabled = status === "thinking" || status === "tool_call"
+    const isInputDisabled = status === "thinking" || status === "tool_call" || !!pendingConfirmation
 
     return (
         <Box flexDirection="column" height="100%">
@@ -154,13 +246,54 @@ export function App({
                 branch={branch}
                 sessionTime={sessionTime}
                 status={status}
+                theme={theme}
             />
-            <Chat messages={messages} isThinking={status === "thinking"} />
+            <Chat
+                messages={messages}
+                isThinking={status === "thinking"}
+                theme={theme}
+                showStats={showStats}
+                showToolCalls={showToolCalls}
+            />
+            {commandResult && (
+                <Box
+                    borderStyle="round"
+                    borderColor={commandResult.success ? "green" : "red"}
+                    paddingX={1}
+                    marginY={1}
+                >
+                    <Text color={commandResult.success ? "green" : "red"} wrap="wrap">
+                        {commandResult.message}
+                    </Text>
+                </Box>
+            )}
+            {pendingConfirmation && (
+                <ConfirmDialog
+                    message={pendingConfirmation.message}
+                    diff={
+                        pendingConfirmation.diff
+                            ? {
+                                  filePath: pendingConfirmation.diff.filePath,
+                                  oldLines: pendingConfirmation.diff.oldLines,
+                                  newLines: pendingConfirmation.diff.newLines,
+                                  startLine: pendingConfirmation.diff.startLine,
+                              }
+                            : undefined
+                    }
+                    onSelect={handleConfirmSelect}
+                    editableContent={pendingConfirmation.diff?.newLines}
+                    syntaxHighlight={syntaxHighlight}
+                />
+            )}
             <Input
                 onSubmit={handleSubmit}
                 history={session?.inputHistory ?? []}
                 disabled={isInputDisabled}
                 placeholder={isInputDisabled ? "Processing..." : "Type a message..."}
+                storage={deps.storage}
+                projectRoot={projectPath}
+                autocompleteEnabled={true}
+                multiline={multiline}
             />
         </Box>
     )

packages/ipuaro/src/tui/components/Chat.tsx

@@ -7,10 +7,14 @@ import { Box, Text } from "ink"
 import type React from "react"
 import type { ChatMessage } from "../../domain/value-objects/ChatMessage.js"
 import type { ToolCall } from "../../domain/value-objects/ToolCall.js"
+import { getRoleColor, type Theme } from "../utils/theme.js"
 
 export interface ChatProps {
     messages: ChatMessage[]
     isThinking: boolean
+    theme?: Theme
+    showStats?: boolean
+    showToolCalls?: boolean
 }
 
 function formatTimestamp(timestamp: number): string {
@@ -42,11 +46,20 @@ function formatToolCall(call: ToolCall): string {
     return `[${call.name} ${params}]`
 }
 
-function UserMessage({ message }: { message: ChatMessage }): React.JSX.Element {
+interface MessageComponentProps {
+    message: ChatMessage
+    theme: Theme
+    showStats: boolean
+    showToolCalls: boolean
+}
+
+function UserMessage({ message, theme }: MessageComponentProps): React.JSX.Element {
+    const roleColor = getRoleColor("user", theme)
+
     return (
         <Box flexDirection="column" marginBottom={1}>
             <Box gap={1}>
-                <Text color="green" bold>
+                <Text color={roleColor} bold>
                     You
                 </Text>
                 <Text color="gray" dimColor>
@@ -60,13 +73,19 @@ function UserMessage({ message }: { message: ChatMessage }): React.JSX.Element {
     )
 }
 
-function AssistantMessage({ message }: { message: ChatMessage }): React.JSX.Element {
+function AssistantMessage({
+    message,
+    theme,
+    showStats,
+    showToolCalls,
+}: MessageComponentProps): React.JSX.Element {
     const stats = formatStats(message.stats)
+    const roleColor = getRoleColor("assistant", theme)
 
     return (
         <Box flexDirection="column" marginBottom={1}>
             <Box gap={1}>
-                <Text color="cyan" bold>
+                <Text color={roleColor} bold>
                     Assistant
                 </Text>
                 <Text color="gray" dimColor>
@@ -74,7 +93,7 @@ function AssistantMessage({ message }: { message: ChatMessage }): React.JSX.Elem
                 </Text>
             </Box>
 
-            {message.toolCalls && message.toolCalls.length > 0 && (
+            {showToolCalls && message.toolCalls && message.toolCalls.length > 0 && (
                 <Box flexDirection="column" marginLeft={2} marginBottom={1}>
                     {message.toolCalls.map((call) => (
                         <Text key={call.id} color="yellow">
@@ -90,7 +109,7 @@ function AssistantMessage({ message }: { message: ChatMessage }): React.JSX.Elem
                 </Box>
             )}
 
-            {stats && (
+            {showStats && stats && (
                 <Box marginLeft={2} marginTop={1}>
                     <Text color="gray" dimColor>
                         {stats}
@@ -101,7 +120,7 @@ function AssistantMessage({ message }: { message: ChatMessage }): React.JSX.Elem
     )
 }
 
-function ToolMessage({ message }: { message: ChatMessage }): React.JSX.Element {
+function ToolMessage({ message }: MessageComponentProps): React.JSX.Element {
     return (
         <Box flexDirection="column" marginBottom={1} marginLeft={2}>
             {message.toolResults?.map((result) => (
@@ -115,31 +134,39 @@ function ToolMessage({ message }: { message: ChatMessage }): React.JSX.Element {
     )
 }
 
-function SystemMessage({ message }: { message: ChatMessage }): React.JSX.Element {
+function SystemMessage({ message, theme }: MessageComponentProps): React.JSX.Element {
     const isError = message.content.toLowerCase().startsWith("error")
+    const roleColor = getRoleColor("system", theme)
 
     return (
         <Box marginBottom={1} marginLeft={2}>
-            <Text color={isError ? "red" : "gray"} dimColor={!isError}>
+            <Text color={isError ? "red" : roleColor} dimColor={!isError}>
                 {message.content}
             </Text>
         </Box>
     )
 }
 
-function MessageComponent({ message }: { message: ChatMessage }): React.JSX.Element {
+function MessageComponent({
+    message,
+    theme,
+    showStats,
+    showToolCalls,
+}: MessageComponentProps): React.JSX.Element {
+    const props = { message, theme, showStats, showToolCalls }
+
     switch (message.role) {
         case "user": {
-            return <UserMessage message={message} />
+            return <UserMessage {...props} />
         }
         case "assistant": {
-            return <AssistantMessage message={message} />
+            return <AssistantMessage {...props} />
         }
         case "tool": {
-            return <ToolMessage message={message} />
+            return <ToolMessage {...props} />
         }
         case "system": {
-            return <SystemMessage message={message} />
+            return <SystemMessage {...props} />
         }
         default: {
             return <></>
@@ -147,24 +174,35 @@ function MessageComponent({ message }: { message: ChatMessage }): React.JSX.Elem
     }
 }
 
-function ThinkingIndicator(): React.JSX.Element {
+function ThinkingIndicator({ theme }: { theme: Theme }): React.JSX.Element {
+    const color = getRoleColor("assistant", theme)
+
     return (
         <Box marginBottom={1}>
-            <Text color="yellow">Thinking...</Text>
+            <Text color={color}>Thinking...</Text>
         </Box>
     )
 }
 
-export function Chat({ messages, isThinking }: ChatProps): React.JSX.Element {
+export function Chat({
+    messages,
+    isThinking,
+    theme = "dark",
+    showStats = true,
+    showToolCalls = true,
+}: ChatProps): React.JSX.Element {
     return (
         <Box flexDirection="column" flexGrow={1} paddingX={1}>
             {messages.map((message, index) => (
                 <MessageComponent
                     key={`${String(message.timestamp)}-${String(index)}`}
                     message={message}
+                    theme={theme}
+                    showStats={showStats}
+                    showToolCalls={showToolCalls}
                 />
             ))}
-            {isThinking && <ThinkingIndicator />}
+            {isThinking && <ThinkingIndicator theme={theme} />}
         </Box>
     )
 }

packages/ipuaro/src/tui/components/ConfirmDialog.tsx

@@ -1,19 +1,25 @@
 /**
  * ConfirmDialog component for TUI.
  * Displays a confirmation dialog with [Y] Apply / [N] Cancel / [E] Edit options.
+ * Supports inline editing when user selects Edit.
  */
 
 import { Box, Text, useInput } from "ink"
-import React, { useState } from "react"
+import React, { useCallback, useState } from "react"
 import type { ConfirmChoice } from "../../shared/types/index.js"
 import { DiffView, type DiffViewProps } from "./DiffView.js"
+import { EditableContent } from "./EditableContent.js"
 
 export interface ConfirmDialogProps {
     message: string
     diff?: DiffViewProps
-    onSelect: (choice: ConfirmChoice) => void
+    onSelect: (choice: ConfirmChoice, editedContent?: string[]) => void
+    editableContent?: string[]
+    syntaxHighlight?: boolean
 }
 
+type DialogMode = "confirm" | "edit"
+
 function ChoiceButton({
     hotkey,
     label,
@@ -32,26 +38,66 @@ function ChoiceButton({
     )
 }
 
-export function ConfirmDialog({ message, diff, onSelect }: ConfirmDialogProps): React.JSX.Element {
+export function ConfirmDialog({
+    message,
+    diff,
+    onSelect,
+    editableContent,
+    syntaxHighlight = false,
+}: ConfirmDialogProps): React.JSX.Element {
+    const [mode, setMode] = useState<DialogMode>("confirm")
     const [selected, setSelected] = useState<ConfirmChoice | null>(null)
 
-    useInput((input, key) => {
-        const lowerInput = input.toLowerCase()
+    const linesToEdit = editableContent ?? diff?.newLines ?? []
+    const canEdit = linesToEdit.length > 0
 
-        if (lowerInput === "y") {
+    const handleEditSubmit = useCallback(
+        (editedLines: string[]) => {
             setSelected("apply")
-            onSelect("apply")
-        } else if (lowerInput === "n") {
-            setSelected("cancel")
-            onSelect("cancel")
-        } else if (lowerInput === "e") {
-            setSelected("edit")
-            onSelect("edit")
-        } else if (key.escape) {
-            setSelected("cancel")
-            onSelect("cancel")
-        }
-    })
+            onSelect("apply", editedLines)
+        },
+        [onSelect],
+    )
+
+    const handleEditCancel = useCallback(() => {
+        setMode("confirm")
+        setSelected(null)
+    }, [])
+
+    useInput(
+        (input, key) => {
+            if (mode === "edit") {
+                return
+            }
+
+            const lowerInput = input.toLowerCase()
+
+            if (lowerInput === "y") {
+                setSelected("apply")
+                onSelect("apply")
+            } else if (lowerInput === "n") {
+                setSelected("cancel")
+                onSelect("cancel")
+            } else if (lowerInput === "e" && canEdit) {
+                setSelected("edit")
+                setMode("edit")
+            } else if (key.escape) {
+                setSelected("cancel")
+                onSelect("cancel")
+            }
+        },
+        { isActive: mode === "confirm" },
+    )
+
+    if (mode === "edit") {
+        return (
+            <EditableContent
+                lines={linesToEdit}
+                onSubmit={handleEditSubmit}
+                onCancel={handleEditCancel}
+            />
+        )
+    }
 
     return (
         <Box
@@ -69,14 +115,22 @@ export function ConfirmDialog({ message, diff, onSelect }: ConfirmDialogProps):
 
             {diff && (
                 <Box marginBottom={1}>
-                    <DiffView {...diff} />
+                    <DiffView {...diff} syntaxHighlight={syntaxHighlight} />
                 </Box>
             )}
 
             <Box gap={2}>
                 <ChoiceButton hotkey="Y" label="Apply" isSelected={selected === "apply"} />
                 <ChoiceButton hotkey="N" label="Cancel" isSelected={selected === "cancel"} />
-                <ChoiceButton hotkey="E" label="Edit" isSelected={selected === "edit"} />
+                {canEdit ? (
+                    <ChoiceButton hotkey="E" label="Edit" isSelected={selected === "edit"} />
+                ) : (
+                    <Box>
+                        <Text color="gray" dimColor>
+                            [E] Edit (disabled)
+                        </Text>
+                    </Box>
+                )}
             </Box>
         </Box>
     )

packages/ipuaro/src/tui/components/DiffView.tsx

@@ -5,12 +5,15 @@
 
 import { Box, Text } from "ink"
 import type React from "react"
+import { detectLanguage, highlightLine, type Language } from "../utils/syntax-highlighter.js"
 
 export interface DiffViewProps {
     filePath: string
     oldLines: string[]
     newLines: string[]
     startLine: number
+    language?: Language
+    syntaxHighlight?: boolean
 }
 
 interface DiffLine {
@@ -97,20 +100,37 @@ function formatLineNumber(num: number | undefined, width: number): string {
 function DiffLine({
     line,
     lineNumberWidth,
+    language,
+    syntaxHighlight,
 }: {
     line: DiffLine
     lineNumberWidth: number
+    language?: Language
+    syntaxHighlight?: boolean
 }): React.JSX.Element {
     const prefix = getLinePrefix(line)
     const color = getLineColor(line)
     const lineNum = formatLineNumber(line.lineNumber, lineNumberWidth)
 
+    const shouldHighlight = syntaxHighlight && language && line.type === "add"
+
     return (
         <Box>
             <Text color="gray">{lineNum} </Text>
-            <Text color={color}>
-                {prefix} {line.content}
-            </Text>
+            {shouldHighlight ? (
+                <Box>
+                    <Text color={color}>{prefix} </Text>
+                    {highlightLine(line.content, language).map((token, idx) => (
+                        <Text key={idx} color={token.color}>
+                            {token.text}
+                        </Text>
+                    ))}
+                </Box>
+            ) : (
+                <Text color={color}>
+                    {prefix} {line.content}
+                </Text>
+            )}
         </Box>
     )
 }
@@ -166,6 +186,8 @@ export function DiffView({
     oldLines,
     newLines,
     startLine,
+    language,
+    syntaxHighlight = false,
 }: DiffViewProps): React.JSX.Element {
     const diffLines = computeDiff(oldLines, newLines, startLine)
     const endLine = startLine + newLines.length - 1
@@ -174,6 +196,8 @@ export function DiffView({
     const additions = diffLines.filter((l) => l.type === "add").length
     const deletions = diffLines.filter((l) => l.type === "remove").length
 
+    const detectedLanguage = language ?? detectLanguage(filePath)
+
     return (
         <Box flexDirection="column" paddingX={1}>
             <DiffHeader filePath={filePath} startLine={startLine} endLine={endLine} />
@@ -183,6 +207,8 @@ export function DiffView({
                         key={`${line.type}-${String(index)}`}
                         line={line}
                         lineNumberWidth={lineNumberWidth}
+                        language={detectedLanguage}
+                        syntaxHighlight={syntaxHighlight}
                     />
                 ))}
             </Box>

packages/ipuaro/src/tui/components/EditableContent.tsx

@@ -0,0 +1,146 @@
+/**
+ * EditableContent component for TUI.
+ * Displays editable multi-line text with line-by-line navigation.
+ */
+
+import { Box, Text, useInput } from "ink"
+import TextInput from "ink-text-input"
+import React, { useCallback, useState } from "react"
+
+export interface EditableContentProps {
+    /** Initial lines to edit */
+    lines: string[]
+    /** Called when user finishes editing (Enter key) */
+    onSubmit: (editedLines: string[]) => void
+    /** Called when user cancels editing (Escape key) */
+    onCancel: () => void
+    /** Maximum visible lines before scrolling */
+    maxVisibleLines?: number
+}
+
+/**
+ * EditableContent component.
+ * Allows line-by-line editing of multi-line text.
+ * - Up/Down: Navigate between lines
+ * - Enter (on last line): Submit changes
+ * - Ctrl+Enter: Submit changes from any line
+ * - Escape: Cancel editing
+ */
+export function EditableContent({
+    lines: initialLines,
+    onSubmit,
+    onCancel,
+    maxVisibleLines = 20,
+}: EditableContentProps): React.JSX.Element {
+    const [lines, setLines] = useState<string[]>(initialLines.length > 0 ? initialLines : [""])
+    const [currentLineIndex, setCurrentLineIndex] = useState(0)
+    const [currentLineValue, setCurrentLineValue] = useState(lines[0] ?? "")
+
+    const updateCurrentLine = useCallback(
+        (value: string) => {
+            const newLines = [...lines]
+            newLines[currentLineIndex] = value
+            setLines(newLines)
+            setCurrentLineValue(value)
+        },
+        [lines, currentLineIndex],
+    )
+
+    const handleLineSubmit = useCallback(() => {
+        updateCurrentLine(currentLineValue)
+
+        if (currentLineIndex === lines.length - 1) {
+            onSubmit(lines)
+        } else {
+            const nextIndex = currentLineIndex + 1
+            setCurrentLineIndex(nextIndex)
+            setCurrentLineValue(lines[nextIndex] ?? "")
+        }
+    }, [currentLineValue, currentLineIndex, lines, updateCurrentLine, onSubmit])
+
+    const handleMoveUp = useCallback(() => {
+        if (currentLineIndex > 0) {
+            updateCurrentLine(currentLineValue)
+            const prevIndex = currentLineIndex - 1
+            setCurrentLineIndex(prevIndex)
+            setCurrentLineValue(lines[prevIndex] ?? "")
+        }
+    }, [currentLineIndex, currentLineValue, lines, updateCurrentLine])
+
+    const handleMoveDown = useCallback(() => {
+        if (currentLineIndex < lines.length - 1) {
+            updateCurrentLine(currentLineValue)
+            const nextIndex = currentLineIndex + 1
+            setCurrentLineIndex(nextIndex)
+            setCurrentLineValue(lines[nextIndex] ?? "")
+        }
+    }, [currentLineIndex, currentLineValue, lines, updateCurrentLine])
+
+    const handleCtrlEnter = useCallback(() => {
+        updateCurrentLine(currentLineValue)
+        onSubmit(lines)
+    }, [currentLineValue, lines, updateCurrentLine, onSubmit])
+
+    useInput(
+        (input, key) => {
+            if (key.escape) {
+                onCancel()
+            } else if (key.upArrow) {
+                handleMoveUp()
+            } else if (key.downArrow) {
+                handleMoveDown()
+            } else if (key.ctrl && key.return) {
+                handleCtrlEnter()
+            }
+        },
+        { isActive: true },
+    )
+
+    const startLine = Math.max(0, currentLineIndex - Math.floor(maxVisibleLines / 2))
+    const endLine = Math.min(lines.length, startLine + maxVisibleLines)
+    const visibleLines = lines.slice(startLine, endLine)
+
+    return (
+        <Box flexDirection="column" borderStyle="round" borderColor="cyan" paddingX={1}>
+            <Box marginBottom={1}>
+                <Text color="cyan" bold>
+                    Edit Content (Line {currentLineIndex + 1}/{lines.length})
+                </Text>
+            </Box>
+
+            <Box flexDirection="column" marginBottom={1}>
+                {visibleLines.map((line, idx) => {
+                    const actualIndex = startLine + idx
+                    const isCurrentLine = actualIndex === currentLineIndex
+
+                    return (
+                        <Box key={actualIndex}>
+                            <Text color="gray" dimColor>
+                                {String(actualIndex + 1).padStart(3, " ")}:{" "}
+                            </Text>
+                            {isCurrentLine ? (
+                                <Box>
+                                    <Text color="cyan">▶ </Text>
+                                    <TextInput
+                                        value={currentLineValue}
+                                        onChange={setCurrentLineValue}
+                                        onSubmit={handleLineSubmit}
+                                    />
+                                </Box>
+                            ) : (
+                                <Text color={isCurrentLine ? "cyan" : "white"}>{line}</Text>
+                            )}
+                        </Box>
+                    )
+                })}
+            </Box>
+
+            <Box flexDirection="column" borderStyle="single" borderColor="gray" paddingX={1}>
+                <Text dimColor>↑/↓: Navigate lines</Text>
+                <Text dimColor>Enter: Next line / Submit (last line)</Text>
+                <Text dimColor>Ctrl+Enter: Submit from any line</Text>
+                <Text dimColor>Escape: Cancel</Text>
+            </Box>
+        </Box>
+    )
+}

packages/ipuaro/src/tui/components/ErrorDialog.tsx

@@ -5,7 +5,7 @@
 
 import { Box, Text, useInput } from "ink"
 import React, { useState } from "react"
-import type { ErrorChoice } from "../../shared/types/index.js"
+import type { ErrorOption } from "../../shared/errors/IpuaroError.js"
 
 export interface ErrorInfo {
     type: string
@@ -15,7 +15,7 @@ export interface ErrorInfo {
 
 export interface ErrorDialogProps {
     error: ErrorInfo
-    onChoice: (choice: ErrorChoice) => void
+    onChoice: (choice: ErrorOption) => void
 }
 
 function ChoiceButton({
@@ -49,7 +49,7 @@ function ChoiceButton({
 }
 
 export function ErrorDialog({ error, onChoice }: ErrorDialogProps): React.JSX.Element {
-    const [selected, setSelected] = useState<ErrorChoice | null>(null)
+    const [selected, setSelected] = useState<ErrorOption | null>(null)
 
     useInput((input, key) => {
         const lowerInput = input.toLowerCase()

packages/ipuaro/src/tui/components/Input.tsx

@@ -6,12 +6,18 @@
 import { Box, Text, useInput } from "ink"
 import TextInput from "ink-text-input"
 import React, { useCallback, useState } from "react"
+import type { IStorage } from "../../domain/services/IStorage.js"
+import { useAutocomplete } from "../hooks/useAutocomplete.js"
 
 export interface InputProps {
     onSubmit: (text: string) => void
     history: string[]
     disabled: boolean
     placeholder?: string
+    storage?: IStorage
+    projectRoot?: string
+    autocompleteEnabled?: boolean
+    multiline?: boolean | "auto"
 }
 
 export function Input({
@@ -19,15 +25,41 @@ export function Input({
     history,
     disabled,
     placeholder = "Type a message...",
+    storage,
+    projectRoot = "",
+    autocompleteEnabled = true,
+    multiline = false,
 }: InputProps): React.JSX.Element {
     const [value, setValue] = useState("")
     const [historyIndex, setHistoryIndex] = useState(-1)
     const [savedInput, setSavedInput] = useState("")
+    const [lines, setLines] = useState<string[]>([""])
+    const [currentLineIndex, setCurrentLineIndex] = useState(0)
 
-    const handleChange = useCallback((newValue: string) => {
-        setValue(newValue)
-        setHistoryIndex(-1)
-    }, [])
+    const isMultilineActive = multiline === true || (multiline === "auto" && lines.length > 1)
+
+    /*
+     * Initialize autocomplete hook if storage is provided
+     * Create a dummy storage object if storage is not provided (autocomplete will be disabled)
+     */
+    const dummyStorage = {} as IStorage
+    const autocomplete = useAutocomplete({
+        storage: storage ?? dummyStorage,
+        projectRoot,
+        enabled: autocompleteEnabled && !!storage,
+    })
+
+    const handleChange = useCallback(
+        (newValue: string) => {
+            setValue(newValue)
+            setHistoryIndex(-1)
+            // Update autocomplete suggestions as user types
+            if (storage && autocompleteEnabled) {
+                autocomplete.complete(newValue)
+            }
+        },
+        [storage, autocompleteEnabled, autocomplete],
+    )
 
     const handleSubmit = useCallback(
         (text: string) => {
@@ -36,63 +68,182 @@ export function Input({
             }
             onSubmit(text)
             setValue("")
+            setLines([""])
+            setCurrentLineIndex(0)
             setHistoryIndex(-1)
             setSavedInput("")
+            autocomplete.reset()
         },
-        [disabled, onSubmit],
+        [disabled, onSubmit, autocomplete],
     )
 
+    const handleLineChange = useCallback(
+        (newValue: string) => {
+            const newLines = [...lines]
+            newLines[currentLineIndex] = newValue
+            setLines(newLines)
+            setValue(newLines.join("\n"))
+        },
+        [lines, currentLineIndex],
+    )
+
+    const handleAddLine = useCallback(() => {
+        const newLines = [...lines]
+        newLines.splice(currentLineIndex + 1, 0, "")
+        setLines(newLines)
+        setCurrentLineIndex(currentLineIndex + 1)
+        setValue(newLines.join("\n"))
+    }, [lines, currentLineIndex])
+
+    const handleMultilineSubmit = useCallback(() => {
+        const fullText = lines.join("\n").trim()
+        if (fullText) {
+            handleSubmit(fullText)
+        }
+    }, [lines, handleSubmit])
+
+    const handleTabKey = useCallback(() => {
+        if (storage && autocompleteEnabled && value.trim()) {
+            const suggestions = autocomplete.suggestions
+            if (suggestions.length > 0) {
+                const completed = autocomplete.accept(value)
+                setValue(completed)
+                autocomplete.complete(completed)
+            }
+        }
+    }, [storage, autocompleteEnabled, value, autocomplete])
+
+    const handleUpArrow = useCallback(() => {
+        if (history.length > 0) {
+            if (historyIndex === -1) {
+                setSavedInput(value)
+            }
+            const newIndex =
+                historyIndex === -1 ? history.length - 1 : Math.max(0, historyIndex - 1)
+            setHistoryIndex(newIndex)
+            setValue(history[newIndex] ?? "")
+            autocomplete.reset()
+        }
+    }, [history, historyIndex, value, autocomplete])
+
+    const handleDownArrow = useCallback(() => {
+        if (historyIndex === -1) {
+            return
+        }
+        if (historyIndex >= history.length - 1) {
+            setHistoryIndex(-1)
+            setValue(savedInput)
+        } else {
+            const newIndex = historyIndex + 1
+            setHistoryIndex(newIndex)
+            setValue(history[newIndex] ?? "")
+        }
+        autocomplete.reset()
+    }, [historyIndex, history, savedInput, autocomplete])
+
     useInput(
         (input, key) => {
             if (disabled) {
                 return
             }
-
-            if (key.upArrow && history.length > 0) {
-                if (historyIndex === -1) {
-                    setSavedInput(value)
-                }
-
-                const newIndex =
-                    historyIndex === -1 ? history.length - 1 : Math.max(0, historyIndex - 1)
-                setHistoryIndex(newIndex)
-                setValue(history[newIndex] ?? "")
+            if (key.tab) {
+                handleTabKey()
             }
-
-            if (key.downArrow) {
-                if (historyIndex === -1) {
-                    return
+            if (key.return && key.shift && isMultilineActive) {
+                handleAddLine()
+            }
+            if (key.upArrow) {
+                if (isMultilineActive && currentLineIndex > 0) {
+                    setCurrentLineIndex(currentLineIndex - 1)
+                } else if (!isMultilineActive) {
+                    handleUpArrow()
                 }
-
-                if (historyIndex >= history.length - 1) {
-                    setHistoryIndex(-1)
-                    setValue(savedInput)
-                } else {
-                    const newIndex = historyIndex + 1
-                    setHistoryIndex(newIndex)
-                    setValue(history[newIndex] ?? "")
+            }
+            if (key.downArrow) {
+                if (isMultilineActive && currentLineIndex < lines.length - 1) {
+                    setCurrentLineIndex(currentLineIndex + 1)
+                } else if (!isMultilineActive) {
+                    handleDownArrow()
                 }
             }
         },
         { isActive: !disabled },
     )
 
+    const hasSuggestions = autocomplete.suggestions.length > 0
+
     return (
-        <Box borderStyle="single" borderColor={disabled ? "gray" : "cyan"} paddingX={1}>
-            <Text color={disabled ? "gray" : "green"} bold>
-                {">"}{" "}
-            </Text>
-            {disabled ? (
-                <Text color="gray" dimColor>
-                    {placeholder}
-                </Text>
-            ) : (
-                <TextInput
-                    value={value}
-                    onChange={handleChange}
-                    onSubmit={handleSubmit}
-                    placeholder={placeholder}
-                />
+        <Box flexDirection="column">
+            <Box
+                borderStyle="single"
+                borderColor={disabled ? "gray" : "cyan"}
+                paddingX={1}
+                flexDirection="column"
+            >
+                {disabled ? (
+                    <Box>
+                        <Text color="gray" bold>
+                            {">"}{" "}
+                        </Text>
+                        <Text color="gray" dimColor>
+                            {placeholder}
+                        </Text>
+                    </Box>
+                ) : isMultilineActive ? (
+                    <Box flexDirection="column">
+                        {lines.map((line, index) => (
+                            <Box key={index}>
+                                <Text color="green" bold>
+                                    {index === currentLineIndex ? ">" : " "}{" "}
+                                </Text>
+                                {index === currentLineIndex ? (
+                                    <TextInput
+                                        value={line}
+                                        onChange={handleLineChange}
+                                        onSubmit={handleMultilineSubmit}
+                                        placeholder={index === 0 ? placeholder : ""}
+                                    />
+                                ) : (
+                                    <Text>{line}</Text>
+                                )}
+                            </Box>
+                        ))}
+                        <Box marginTop={1}>
+                            <Text dimColor>Shift+Enter: new line | Enter: submit</Text>
+                        </Box>
+                    </Box>
+                ) : (
+                    <Box>
+                        <Text color="green" bold>
+                            {">"}{" "}
+                        </Text>
+                        <TextInput
+                            value={value}
+                            onChange={handleChange}
+                            onSubmit={handleSubmit}
+                            placeholder={placeholder}
+                        />
+                    </Box>
+                )}
+            </Box>
+            {hasSuggestions && !disabled && (
+                <Box paddingLeft={2} flexDirection="column">
+                    <Text dimColor>
+                        {autocomplete.suggestions.length === 1
+                            ? "Press Tab to complete"
+                            : `${String(autocomplete.suggestions.length)} suggestions (Tab to complete)`}
+                    </Text>
+                    {autocomplete.suggestions.slice(0, 5).map((suggestion, i) => (
+                        <Text key={i} dimColor color="cyan">
+                            {"  "}• {suggestion}
+                        </Text>
+                    ))}
+                    {autocomplete.suggestions.length > 5 && (
+                        <Text dimColor>
+                            {"  "}... and {String(autocomplete.suggestions.length - 5)} more
+                        </Text>
+                    )}
+                </Box>
             )}
         </Box>
     )

packages/ipuaro/src/tui/components/StatusBar.tsx

@@ -6,6 +6,7 @@
 import { Box, Text } from "ink"
 import type React from "react"
 import type { BranchInfo, TuiStatus } from "../types.js"
+import { getContextColor, getStatusColor, type Theme } from "../utils/theme.js"
 
 export interface StatusBarProps {
     contextUsage: number
@@ -13,27 +14,30 @@ export interface StatusBarProps {
     branch: BranchInfo
     sessionTime: string
     status: TuiStatus
+    theme?: Theme
 }
 
-function getStatusIndicator(status: TuiStatus): { text: string; color: string } {
+function getStatusIndicator(status: TuiStatus, theme: Theme): { text: string; color: string } {
+    const color = getStatusColor(status, theme)
+
     switch (status) {
         case "ready": {
-            return { text: "ready", color: "green" }
+            return { text: "ready", color }
         }
         case "thinking": {
-            return { text: "thinking...", color: "yellow" }
+            return { text: "thinking...", color }
         }
         case "tool_call": {
-            return { text: "executing...", color: "cyan" }
+            return { text: "executing...", color }
         }
         case "awaiting_confirmation": {
-            return { text: "confirm?", color: "magenta" }
+            return { text: "confirm?", color }
         }
         case "error": {
-            return { text: "error", color: "red" }
+            return { text: "error", color }
         }
         default: {
-            return { text: "ready", color: "green" }
+            return { text: "ready", color }
         }
     }
 }
@@ -48,9 +52,11 @@ export function StatusBar({
     branch,
     sessionTime,
     status,
+    theme = "dark",
 }: StatusBarProps): React.JSX.Element {
-    const statusIndicator = getStatusIndicator(status)
+    const statusIndicator = getStatusIndicator(status, theme)
     const branchDisplay = branch.isDetached ? `HEAD@${branch.name.slice(0, 7)}` : branch.name
+    const contextColor = getContextColor(contextUsage, theme)
 
     return (
         <Box borderStyle="single" borderColor="gray" paddingX={1} justifyContent="space-between">
@@ -59,11 +65,7 @@ export function StatusBar({
                     [ipuaro]
                 </Text>
                 <Text color="gray">
-                    [ctx:{" "}
-                    <Text color={contextUsage > 0.8 ? "red" : "white"}>
-                        {formatContextUsage(contextUsage)}
-                    </Text>
-                    ]
+                    [ctx: <Text color={contextColor}>{formatContextUsage(contextUsage)}</Text>]
                 </Text>
                 <Text color="gray">
                     [<Text color="blue">{projectName}</Text>]

packages/ipuaro/src/tui/components/index.ts

@@ -9,3 +9,4 @@ export { DiffView, type DiffViewProps } from "./DiffView.js"
 export { ConfirmDialog, type ConfirmDialogProps } from "./ConfirmDialog.js"
 export { ErrorDialog, type ErrorDialogProps, type ErrorInfo } from "./ErrorDialog.js"
 export { Progress, type ProgressProps } from "./Progress.js"
+export { EditableContent, type EditableContentProps } from "./EditableContent.js"

packages/ipuaro/src/tui/hooks/index.ts

@@ -9,3 +9,18 @@ export {
     type UseSessionReturn,
 } from "./useSession.js"
 export { useHotkeys, type HotkeyHandlers, type UseHotkeysOptions } from "./useHotkeys.js"
+export {
+    useCommands,
+    parseCommand,
+    type UseCommandsDependencies,
+    type UseCommandsActions,
+    type UseCommandsOptions,
+    type UseCommandsReturn,
+    type CommandResult,
+    type CommandDefinition,
+} from "./useCommands.js"
+export {
+    useAutocomplete,
+    type UseAutocompleteOptions,
+    type UseAutocompleteReturn,
+} from "./useAutocomplete.js"

packages/ipuaro/src/tui/hooks/useAutocomplete.ts

@@ -0,0 +1,204 @@
+/**
+ * useAutocomplete hook for file path autocomplete.
+ * Provides Tab completion for file paths using Redis index.
+ */
+
+import { useCallback, useEffect, useState } from "react"
+import type { IStorage } from "../../domain/services/IStorage.js"
+import type { AutocompleteConfig } from "../../shared/constants/config.js"
+import path from "node:path"
+
+export interface UseAutocompleteOptions {
+    storage: IStorage
+    projectRoot: string
+    enabled?: boolean
+    maxSuggestions?: number
+    config?: AutocompleteConfig
+}
+
+export interface UseAutocompleteReturn {
+    suggestions: string[]
+    complete: (partial: string) => string[]
+    accept: (suggestion: string) => string
+    reset: () => void
+}
+
+/**
+ * Normalizes a path by removing leading ./ and trailing /
+ */
+function normalizePath(p: string): string {
+    let normalized = p.trim()
+    if (normalized.startsWith("./")) {
+        normalized = normalized.slice(2)
+    }
+    if (normalized.endsWith("/") && normalized.length > 1) {
+        normalized = normalized.slice(0, -1)
+    }
+    return normalized
+}
+
+/**
+ * Calculates fuzzy match score between partial and candidate.
+ * Returns 0 if no match, higher score for better matches.
+ */
+function fuzzyScore(partial: string, candidate: string): number {
+    const partialLower = partial.toLowerCase()
+    const candidateLower = candidate.toLowerCase()
+
+    // Exact prefix match gets highest score
+    if (candidateLower.startsWith(partialLower)) {
+        return 1000 + (1000 - partial.length)
+    }
+
+    // Check if all characters from partial appear in order in candidate
+    let partialIndex = 0
+    let candidateIndex = 0
+    let lastMatchIndex = -1
+    let consecutiveMatches = 0
+
+    while (partialIndex < partialLower.length && candidateIndex < candidateLower.length) {
+        if (partialLower[partialIndex] === candidateLower[candidateIndex]) {
+            // Bonus for consecutive matches
+            if (candidateIndex === lastMatchIndex + 1) {
+                consecutiveMatches++
+            } else {
+                consecutiveMatches = 0
+            }
+            lastMatchIndex = candidateIndex
+            partialIndex++
+        }
+        candidateIndex++
+    }
+
+    // If we didn't match all characters, no match
+    if (partialIndex < partialLower.length) {
+        return 0
+    }
+
+    // Score based on how tight the match is
+    const matchSpread = lastMatchIndex - (partialLower.length - 1)
+    const score = 100 + consecutiveMatches * 10 - matchSpread
+
+    return Math.max(0, score)
+}
+
+/**
+ * Gets the common prefix of all suggestions
+ */
+function getCommonPrefix(suggestions: string[]): string {
+    if (suggestions.length === 0) {
+        return ""
+    }
+    if (suggestions.length === 1) {
+        return suggestions[0] ?? ""
+    }
+
+    let prefix = suggestions[0] ?? ""
+    for (let i = 1; i < suggestions.length; i++) {
+        const current = suggestions[i] ?? ""
+        let j = 0
+        while (j < prefix.length && j < current.length && prefix[j] === current[j]) {
+            j++
+        }
+        prefix = prefix.slice(0, j)
+        if (prefix.length === 0) {
+            break
+        }
+    }
+    return prefix
+}
+
+export function useAutocomplete(options: UseAutocompleteOptions): UseAutocompleteReturn {
+    const { storage, projectRoot, enabled, maxSuggestions, config } = options
+
+    // Read from config if provided, otherwise use options, otherwise use defaults
+    const isEnabled = config?.enabled ?? enabled ?? true
+    const maxSuggestionsCount = config?.maxSuggestions ?? maxSuggestions ?? 10
+
+    const [filePaths, setFilePaths] = useState<string[]>([])
+    const [suggestions, setSuggestions] = useState<string[]>([])
+
+    // Load file paths from storage
+    useEffect(() => {
+        if (!isEnabled) {
+            return
+        }
+
+        const loadPaths = async (): Promise<void> => {
+            try {
+                const files = await storage.getAllFiles()
+                const paths = Array.from(files.keys()).map((p) => {
+                    // Make paths relative to project root
+                    const relative = path.relative(projectRoot, p)
+                    return normalizePath(relative)
+                })
+                setFilePaths(paths.sort())
+            } catch {
+                // Silently fail - autocomplete is non-critical
+                setFilePaths([])
+            }
+        }
+
+        loadPaths().catch(() => {
+            // Ignore errors
+        })
+    }, [storage, projectRoot, isEnabled])
+
+    const complete = useCallback(
+        (partial: string): string[] => {
+            if (!isEnabled || !partial.trim()) {
+                setSuggestions([])
+                return []
+            }
+
+            const normalized = normalizePath(partial)
+
+            // Score and filter matches
+            const scored = filePaths
+                .map((p) => ({
+                    path: p,
+                    score: fuzzyScore(normalized, p),
+                }))
+                .filter((item) => item.score > 0)
+                .sort((a, b) => b.score - a.score)
+                .slice(0, maxSuggestionsCount)
+                .map((item) => item.path)
+
+            setSuggestions(scored)
+            return scored
+        },
+        [isEnabled, filePaths, maxSuggestionsCount],
+    )
+
+    const accept = useCallback(
+        (suggestion: string): string => {
+            // If there's only one suggestion, complete with it
+            if (suggestions.length === 1) {
+                setSuggestions([])
+                return suggestions[0] ?? ""
+            }
+
+            // If there are multiple suggestions, complete with common prefix
+            if (suggestions.length > 1) {
+                const prefix = getCommonPrefix(suggestions)
+                if (prefix.length > suggestion.length) {
+                    return prefix
+                }
+            }
+
+            return suggestion
+        },
+        [suggestions],
+    )
+
+    const reset = useCallback(() => {
+        setSuggestions([])
+    }, [])
+
+    return {
+        suggestions,
+        complete,
+        accept,
+        reset,
+    }
+}

packages/ipuaro/src/tui/hooks/useCommands.ts

@@ -0,0 +1,444 @@
+/**
+ * useCommands hook for TUI.
+ * Handles slash commands (/help, /clear, /undo, etc.)
+ */
+
+import { useCallback, useMemo } from "react"
+import type { Session } from "../../domain/entities/Session.js"
+import type { ILLMClient } from "../../domain/services/ILLMClient.js"
+import type { ISessionStorage } from "../../domain/services/ISessionStorage.js"
+import type { IStorage } from "../../domain/services/IStorage.js"
+import type { IToolRegistry } from "../../application/interfaces/IToolRegistry.js"
+
+/**
+ * Command result returned after execution.
+ */
+export interface CommandResult {
+    success: boolean
+    message: string
+    data?: unknown
+}
+
+/**
+ * Command definition.
+ */
+export interface CommandDefinition {
+    name: string
+    description: string
+    usage: string
+    execute: (args: string[]) => Promise<CommandResult>
+}
+
+/**
+ * Dependencies for useCommands hook.
+ */
+export interface UseCommandsDependencies {
+    session: Session | null
+    sessionStorage: ISessionStorage
+    storage: IStorage
+    llm: ILLMClient
+    tools: IToolRegistry
+    projectRoot: string
+    projectName: string
+}
+
+/**
+ * Actions provided by the parent component.
+ */
+export interface UseCommandsActions {
+    clearHistory: () => void
+    undo: () => Promise<boolean>
+    setAutoApply: (value: boolean) => void
+    reindex: () => Promise<void>
+}
+
+/**
+ * Options for useCommands hook.
+ */
+export interface UseCommandsOptions {
+    autoApply: boolean
+}
+
+/**
+ * Return type for useCommands hook.
+ */
+export interface UseCommandsReturn {
+    executeCommand: (input: string) => Promise<CommandResult | null>
+    isCommand: (input: string) => boolean
+    getCommands: () => CommandDefinition[]
+}
+
+/**
+ * Parses command input into command name and arguments.
+ */
+export function parseCommand(input: string): { command: string; args: string[] } | null {
+    const trimmed = input.trim()
+    if (!trimmed.startsWith("/")) {
+        return null
+    }
+
+    const parts = trimmed.slice(1).split(/\s+/)
+    const command = parts[0]?.toLowerCase() ?? ""
+    const args = parts.slice(1)
+
+    return { command, args }
+}
+
+// Command factory functions to keep the hook clean and under line limits
+
+function createHelpCommand(map: Map<string, CommandDefinition>): CommandDefinition {
+    return {
+        name: "help",
+        description: "Shows all commands and hotkeys",
+        usage: "/help",
+        execute: async (): Promise<CommandResult> => {
+            const commandList = Array.from(map.values())
+                .map((cmd) => `  ${cmd.usage.padEnd(25)} ${cmd.description}`)
+                .join("\n")
+
+            const hotkeys = [
+                "  Ctrl+C (1x)              Interrupt current operation",
+                "  Ctrl+C (2x)              Exit ipuaro",
+                "  Ctrl+D                   Exit with session save",
+                "  Ctrl+Z                   Undo last change",
+                "  ↑/↓                      Navigate input history",
+            ].join("\n")
+
+            const message = ["Available commands:", commandList, "", "Hotkeys:", hotkeys].join("\n")
+
+            return Promise.resolve({ success: true, message })
+        },
+    }
+}
+
+function createClearCommand(actions: UseCommandsActions): CommandDefinition {
+    return {
+        name: "clear",
+        description: "Clears chat history (keeps session)",
+        usage: "/clear",
+        execute: async (): Promise<CommandResult> => {
+            actions.clearHistory()
+            return Promise.resolve({ success: true, message: "Chat history cleared." })
+        },
+    }
+}
+
+function createUndoCommand(
+    deps: UseCommandsDependencies,
+    actions: UseCommandsActions,
+): CommandDefinition {
+    return {
+        name: "undo",
+        description: "Reverts last file change",
+        usage: "/undo",
+        execute: async (): Promise<CommandResult> => {
+            if (!deps.session) {
+                return { success: false, message: "No active session." }
+            }
+
+            const undoStack = deps.session.undoStack
+            if (undoStack.length === 0) {
+                return { success: false, message: "Nothing to undo." }
+            }
+
+            const result = await actions.undo()
+            if (result) {
+                return { success: true, message: "Last change reverted." }
+            }
+            return { success: false, message: "Failed to undo. File may have been modified." }
+        },
+    }
+}
+
+function createSessionsCommand(deps: UseCommandsDependencies): CommandDefinition {
+    return {
+        name: "sessions",
+        description: "Manage sessions (list, load <id>, delete <id>)",
+        usage: "/sessions [list|load|delete] [id]",
+        execute: async (args: string[]): Promise<CommandResult> => {
+            const subCommand = args[0]?.toLowerCase() ?? "list"
+
+            if (subCommand === "list") {
+                return handleSessionsList(deps)
+            }
+
+            if (subCommand === "load") {
+                return handleSessionsLoad(deps, args[1])
+            }
+
+            if (subCommand === "delete") {
+                return handleSessionsDelete(deps, args[1])
+            }
+
+            return { success: false, message: "Usage: /sessions [list|load|delete] [id]" }
+        },
+    }
+}
+
+async function handleSessionsList(deps: UseCommandsDependencies): Promise<CommandResult> {
+    const sessions = await deps.sessionStorage.listSessions(deps.projectName)
+    if (sessions.length === 0) {
+        return { success: true, message: "No sessions found." }
+    }
+
+    const currentId = deps.session?.id
+    const sessionList = sessions
+        .map((s) => {
+            const current = s.id === currentId ? " (current)" : ""
+            const date = new Date(s.createdAt).toLocaleString()
+            return `  ${s.id.slice(0, 8)}${current} - ${date} - ${String(s.messageCount)} messages`
+        })
+        .join("\n")
+
+    return {
+        success: true,
+        message: `Sessions for ${deps.projectName}:\n${sessionList}`,
+        data: sessions,
+    }
+}
+
+async function handleSessionsLoad(
+    deps: UseCommandsDependencies,
+    sessionId: string | undefined,
+): Promise<CommandResult> {
+    if (!sessionId) {
+        return { success: false, message: "Usage: /sessions load <id>" }
+    }
+
+    const exists = await deps.sessionStorage.sessionExists(sessionId)
+    if (!exists) {
+        return { success: false, message: `Session ${sessionId} not found.` }
+    }
+
+    return {
+        success: true,
+        message: `To load session ${sessionId}, restart ipuaro with --session ${sessionId}`,
+        data: { sessionId },
+    }
+}
+
+async function handleSessionsDelete(
+    deps: UseCommandsDependencies,
+    sessionId: string | undefined,
+): Promise<CommandResult> {
+    if (!sessionId) {
+        return { success: false, message: "Usage: /sessions delete <id>" }
+    }
+
+    if (deps.session?.id === sessionId) {
+        return { success: false, message: "Cannot delete current session." }
+    }
+
+    const exists = await deps.sessionStorage.sessionExists(sessionId)
+    if (!exists) {
+        return { success: false, message: `Session ${sessionId} not found.` }
+    }
+
+    await deps.sessionStorage.deleteSession(sessionId)
+    return { success: true, message: `Session ${sessionId} deleted.` }
+}
+
+function createStatusCommand(
+    deps: UseCommandsDependencies,
+    options: UseCommandsOptions,
+): CommandDefinition {
+    return {
+        name: "status",
+        description: "Shows system and session status",
+        usage: "/status",
+        execute: async (): Promise<CommandResult> => {
+            const llmAvailable = await deps.llm.isAvailable()
+            const llmStatus = llmAvailable ? "connected" : "unavailable"
+
+            const contextUsage = deps.session?.context.tokenUsage ?? 0
+            const contextPercent = Math.round(contextUsage * 100)
+
+            const sessionStats = deps.session?.stats ?? {
+                totalTokens: 0,
+                totalTime: 0,
+                toolCalls: 0,
+                editsApplied: 0,
+                editsRejected: 0,
+            }
+
+            const undoCount = deps.session?.undoStack.length ?? 0
+
+            const message = [
+                "System Status:",
+                `  LLM:          ${llmStatus}`,
+                `  Context:      ${String(contextPercent)}% used`,
+                `  Auto-apply:   ${options.autoApply ? "on" : "off"}`,
+                "",
+                "Session Stats:",
+                `  Tokens:       ${sessionStats.totalTokens.toLocaleString()}`,
+                `  Tool calls:   ${String(sessionStats.toolCalls)}`,
+                `  Edits:        ${String(sessionStats.editsApplied)} applied, ${String(sessionStats.editsRejected)} rejected`,
+                `  Undo stack:   ${String(undoCount)} entries`,
+                "",
+                "Project:",
+                `  Name:         ${deps.projectName}`,
+                `  Root:         ${deps.projectRoot}`,
+            ].join("\n")
+
+            return { success: true, message }
+        },
+    }
+}
+
+function createReindexCommand(actions: UseCommandsActions): CommandDefinition {
+    return {
+        name: "reindex",
+        description: "Forces full project reindexation",
+        usage: "/reindex",
+        execute: async (): Promise<CommandResult> => {
+            try {
+                await actions.reindex()
+                return { success: true, message: "Project reindexed successfully." }
+            } catch (err) {
+                const errorMessage = err instanceof Error ? err.message : String(err)
+                return { success: false, message: `Reindex failed: ${errorMessage}` }
+            }
+        },
+    }
+}
+
+function createEvalCommand(deps: UseCommandsDependencies): CommandDefinition {
+    return {
+        name: "eval",
+        description: "LLM self-check for hallucinations",
+        usage: "/eval",
+        execute: async (): Promise<CommandResult> => {
+            if (!deps.session || deps.session.history.length === 0) {
+                return { success: false, message: "No conversation to evaluate." }
+            }
+
+            const lastAssistantMessage = [...deps.session.history]
+                .reverse()
+                .find((m) => m.role === "assistant")
+
+            if (!lastAssistantMessage) {
+                return { success: false, message: "No assistant response to evaluate." }
+            }
+
+            const evalPrompt = [
+                "Review your last response for potential issues:",
+                "1. Are there any factual errors or hallucinations?",
+                "2. Did you reference files or code that might not exist?",
+                "3. Are there any assumptions that should be verified?",
+                "",
+                "Last response to evaluate:",
+                lastAssistantMessage.content.slice(0, 2000),
+            ].join("\n")
+
+            try {
+                const response = await deps.llm.chat([
+                    { role: "user", content: evalPrompt, timestamp: Date.now() },
+                ])
+
+                return {
+                    success: true,
+                    message: `Self-evaluation:\n${response.content}`,
+                    data: { evaluated: lastAssistantMessage.content.slice(0, 100) },
+                }
+            } catch (err) {
+                const errorMessage = err instanceof Error ? err.message : String(err)
+                return { success: false, message: `Evaluation failed: ${errorMessage}` }
+            }
+        },
+    }
+}
+
+function createAutoApplyCommand(
+    actions: UseCommandsActions,
+    options: UseCommandsOptions,
+): CommandDefinition {
+    return {
+        name: "auto-apply",
+        description: "Toggle auto-apply mode (on/off)",
+        usage: "/auto-apply [on|off]",
+        execute: async (args: string[]): Promise<CommandResult> => {
+            const arg = args[0]?.toLowerCase()
+
+            if (arg === "on") {
+                actions.setAutoApply(true)
+                return Promise.resolve({ success: true, message: "Auto-apply enabled." })
+            }
+
+            if (arg === "off") {
+                actions.setAutoApply(false)
+                return Promise.resolve({ success: true, message: "Auto-apply disabled." })
+            }
+
+            if (!arg) {
+                const current = options.autoApply ? "on" : "off"
+                return Promise.resolve({
+                    success: true,
+                    message: `Auto-apply is currently: ${current}`,
+                })
+            }
+
+            return Promise.resolve({ success: false, message: "Usage: /auto-apply [on|off]" })
+        },
+    }
+}
+
+/**
+ * Hook for handling slash commands in TUI.
+ */
+export function useCommands(
+    deps: UseCommandsDependencies,
+    actions: UseCommandsActions,
+    options: UseCommandsOptions,
+): UseCommandsReturn {
+    const commands = useMemo((): Map<string, CommandDefinition> => {
+        const map = new Map<string, CommandDefinition>()
+
+        // Register all commands
+        const helpCmd = createHelpCommand(map)
+        map.set("help", helpCmd)
+        map.set("clear", createClearCommand(actions))
+        map.set("undo", createUndoCommand(deps, actions))
+        map.set("sessions", createSessionsCommand(deps))
+        map.set("status", createStatusCommand(deps, options))
+        map.set("reindex", createReindexCommand(actions))
+        map.set("eval", createEvalCommand(deps))
+        map.set("auto-apply", createAutoApplyCommand(actions, options))
+
+        return map
+    }, [deps, actions, options])
+
+    const isCommand = useCallback((input: string): boolean => {
+        return input.trim().startsWith("/")
+    }, [])
+
+    const executeCommand = useCallback(
+        async (input: string): Promise<CommandResult | null> => {
+            const parsed = parseCommand(input)
+            if (!parsed) {
+                return null
+            }
+
+            const command = commands.get(parsed.command)
+            if (!command) {
+                const available = Array.from(commands.keys()).join(", ")
+                return {
+                    success: false,
+                    message: `Unknown command: /${parsed.command}\nAvailable: ${available}`,
+                }
+            }
+
+            return command.execute(parsed.args)
+        },
+        [commands],
+    )
+
+    const getCommands = useCallback((): CommandDefinition[] => {
+        return Array.from(commands.values())
+    }, [commands])
+
+    return {
+        executeCommand,
+        isCommand,
+        getCommands,
+    }
+}

packages/ipuaro/src/tui/hooks/useSession.ts

@@ -10,7 +10,8 @@ import type { ISessionStorage } from "../../domain/services/ISessionStorage.js"
 import type { IStorage } from "../../domain/services/IStorage.js"
 import type { DiffInfo } from "../../domain/services/ITool.js"
 import type { ChatMessage } from "../../domain/value-objects/ChatMessage.js"
-import type { ErrorChoice } from "../../shared/types/index.js"
+import type { ErrorOption } from "../../shared/errors/IpuaroError.js"
+import type { Config } from "../../shared/constants/config.js"
 import type { IToolRegistry } from "../../application/interfaces/IToolRegistry.js"
 import {
     HandleMessage,
@@ -18,6 +19,7 @@ import {
 } from "../../application/use-cases/HandleMessage.js"
 import { StartSession } from "../../application/use-cases/StartSession.js"
 import { UndoChange } from "../../application/use-cases/UndoChange.js"
+import type { ConfirmationResult } from "../../application/use-cases/ExecuteTool.js"
 import type { ProjectStructure } from "../../infrastructure/llm/prompts.js"
 import type { TuiStatus } from "../types.js"
 
@@ -29,12 +31,13 @@ export interface UseSessionDependencies {
     projectRoot: string
     projectName: string
     projectStructure?: ProjectStructure
+    config?: Config
 }
 
 export interface UseSessionOptions {
     autoApply?: boolean
-    onConfirmation?: (message: string, diff?: DiffInfo) => Promise<boolean>
-    onError?: (error: Error) => Promise<ErrorChoice>
+    onConfirmation?: (message: string, diff?: DiffInfo) => Promise<boolean | ConfirmationResult>
+    onError?: (error: Error) => Promise<ErrorOption>
 }
 
 export interface UseSessionReturn {
@@ -106,11 +109,17 @@ async function initializeSession(
         deps.llm,
         deps.tools,
         deps.projectRoot,
+        deps.config?.context,
     )
     if (deps.projectStructure) {
         handleMessage.setProjectStructure(deps.projectStructure)
     }
-    handleMessage.setOptions({ autoApply: options.autoApply })
+    handleMessage.setOptions({
+        autoApply: options.autoApply,
+        maxHistoryMessages: deps.config?.session.maxHistoryMessages,
+        saveInputHistory: deps.config?.session.saveInputHistory,
+        contextConfig: deps.config?.context,
+    })
     handleMessage.setEvents(createEventHandlers(setters, options))
     refs.current.handleMessage = handleMessage
     refs.current.undoChange = new UndoChange(deps.sessionStorage, deps.storage)

packages/ipuaro/src/tui/utils/bell.ts

@@ -0,0 +1,11 @@
+/**
+ * Bell notification utility for terminal.
+ */
+
+/**
+ * Ring the terminal bell.
+ * Works by outputting the ASCII bell character (\u0007).
+ */
+export function ringBell(): void {
+    process.stdout.write("\u0007")
+}

packages/ipuaro/src/tui/utils/syntax-highlighter.ts

@@ -0,0 +1,167 @@
+/**
+ * Simple syntax highlighter for terminal UI.
+ * Highlights keywords, strings, comments, numbers, and operators.
+ */
+
+export type Language = "typescript" | "javascript" | "tsx" | "jsx" | "json" | "yaml" | "unknown"
+
+export interface HighlightedToken {
+    text: string
+    color: string
+}
+
+const KEYWORDS = new Set([
+    "abstract",
+    "any",
+    "as",
+    "async",
+    "await",
+    "boolean",
+    "break",
+    "case",
+    "catch",
+    "class",
+    "const",
+    "constructor",
+    "continue",
+    "debugger",
+    "declare",
+    "default",
+    "delete",
+    "do",
+    "else",
+    "enum",
+    "export",
+    "extends",
+    "false",
+    "finally",
+    "for",
+    "from",
+    "function",
+    "get",
+    "if",
+    "implements",
+    "import",
+    "in",
+    "instanceof",
+    "interface",
+    "let",
+    "module",
+    "namespace",
+    "new",
+    "null",
+    "number",
+    "of",
+    "package",
+    "private",
+    "protected",
+    "public",
+    "readonly",
+    "require",
+    "return",
+    "set",
+    "static",
+    "string",
+    "super",
+    "switch",
+    "this",
+    "throw",
+    "true",
+    "try",
+    "type",
+    "typeof",
+    "undefined",
+    "var",
+    "void",
+    "while",
+    "with",
+    "yield",
+])
+
+export function detectLanguage(filePath: string): Language {
+    const ext = filePath.split(".").pop()?.toLowerCase()
+    switch (ext) {
+        case "ts":
+            return "typescript"
+        case "tsx":
+            return "tsx"
+        case "js":
+            return "javascript"
+        case "jsx":
+            return "jsx"
+        case "json":
+            return "json"
+        case "yaml":
+        case "yml":
+            return "yaml"
+        default:
+            return "unknown"
+    }
+}
+
+const COMMENT_REGEX = /^(\/\/.*|\/\*[\s\S]*?\*\/)/
+const STRING_REGEX = /^("(?:[^"\\]|\\.)*"|'(?:[^'\\]|\\.)*'|`(?:[^`\\]|\\.)*`)/
+const NUMBER_REGEX = /^(\b\d+\.?\d*\b)/
+const WORD_REGEX = /^([a-zA-Z_$][a-zA-Z0-9_$]*)/
+const OPERATOR_REGEX = /^([+\-*/%=<>!&|^~?:;,.()[\]{}])/
+const WHITESPACE_REGEX = /^(\s+)/
+
+export function highlightLine(line: string, language: Language): HighlightedToken[] {
+    if (language === "unknown" || language === "json" || language === "yaml") {
+        return [{ text: line, color: "white" }]
+    }
+
+    const tokens: HighlightedToken[] = []
+    let remaining = line
+
+    while (remaining.length > 0) {
+        const commentMatch = COMMENT_REGEX.exec(remaining)
+        if (commentMatch) {
+            tokens.push({ text: commentMatch[0], color: "gray" })
+            remaining = remaining.slice(commentMatch[0].length)
+            continue
+        }
+
+        const stringMatch = STRING_REGEX.exec(remaining)
+        if (stringMatch) {
+            tokens.push({ text: stringMatch[0], color: "green" })
+            remaining = remaining.slice(stringMatch[0].length)
+            continue
+        }
+
+        const numberMatch = NUMBER_REGEX.exec(remaining)
+        if (numberMatch) {
+            tokens.push({ text: numberMatch[0], color: "cyan" })
+            remaining = remaining.slice(numberMatch[0].length)
+            continue
+        }
+
+        const wordMatch = WORD_REGEX.exec(remaining)
+        if (wordMatch) {
+            const word = wordMatch[0]
+            const color = KEYWORDS.has(word) ? "magenta" : "white"
+            tokens.push({ text: word, color })
+            remaining = remaining.slice(word.length)
+            continue
+        }
+
+        const operatorMatch = OPERATOR_REGEX.exec(remaining)
+        if (operatorMatch) {
+            tokens.push({ text: operatorMatch[0], color: "yellow" })
+            remaining = remaining.slice(operatorMatch[0].length)
+            continue
+        }
+
+        const whitespaceMatch = WHITESPACE_REGEX.exec(remaining)
+        if (whitespaceMatch) {
+            tokens.push({ text: whitespaceMatch[0], color: "white" })
+            remaining = remaining.slice(whitespaceMatch[0].length)
+            continue
+        }
+
+        tokens.push({ text: remaining[0] ?? "", color: "white" })
+        remaining = remaining.slice(1)
+    }
+
+    return tokens
+}

packages/ipuaro/src/tui/utils/theme.ts

@@ -0,0 +1,115 @@
+/**
+ * Theme color utilities for TUI.
+ */
+
+export type Theme = "dark" | "light"
+
+/**
+ * Color scheme for a theme.
+ */
+export interface ColorScheme {
+    primary: string
+    secondary: string
+    success: string
+    warning: string
+    error: string
+    info: string
+    muted: string
+    background: string
+    foreground: string
+}
+
+/**
+ * Dark theme color scheme (default).
+ */
+const DARK_THEME: ColorScheme = {
+    primary: "cyan",
+    secondary: "blue",
+    success: "green",
+    warning: "yellow",
+    error: "red",
+    info: "cyan",
+    muted: "gray",
+    background: "black",
+    foreground: "white",
+}
+
+/**
+ * Light theme color scheme.
+ */
+const LIGHT_THEME: ColorScheme = {
+    primary: "blue",
+    secondary: "cyan",
+    success: "green",
+    warning: "yellow",
+    error: "red",
+    info: "blue",
+    muted: "gray",
+    background: "white",
+    foreground: "black",
+}
+
+/**
+ * Get color scheme for a theme.
+ */
+export function getColorScheme(theme: Theme): ColorScheme {
+    return theme === "dark" ? DARK_THEME : LIGHT_THEME
+}
+
+/**
+ * Get color for a status.
+ */
+export function getStatusColor(
+    status: "ready" | "thinking" | "error" | "tool_call" | "awaiting_confirmation",
+    theme: Theme = "dark",
+): string {
+    const scheme = getColorScheme(theme)
+
+    switch (status) {
+        case "ready":
+            return scheme.success
+        case "thinking":
+        case "tool_call":
+            return scheme.warning
+        case "awaiting_confirmation":
+            return scheme.info
+        case "error":
+            return scheme.error
+    }
+}
+
+/**
+ * Get color for a message role.
+ */
+export function getRoleColor(
+    role: "user" | "assistant" | "system" | "tool",
+    theme: Theme = "dark",
+): string {
+    const scheme = getColorScheme(theme)
+
+    switch (role) {
+        case "user":
+            return scheme.success
+        case "assistant":
+            return scheme.primary
+        case "system":
+            return scheme.muted
+        case "tool":
+            return scheme.secondary
+    }
+}
+
+/**
+ * Get color for context usage percentage.
+ */
+export function getContextColor(usage: number, theme: Theme = "dark"): string {
+    const scheme = getColorScheme(theme)
+
+    if (usage >= 0.8) {
+        return scheme.error
+    }
+    if (usage >= 0.6) {
+        return scheme.warning
+    }
+    return scheme.success
+}

packages/ipuaro/tests/e2e/test-helpers.ts

@@ -0,0 +1,351 @@
+/**
+ * E2E Test Helpers
+ * Provides dependencies for testing the full flow with REAL LLM.
+ */
+
+import { vi } from "vitest"
+import * as fs from "node:fs/promises"
+import * as path from "node:path"
+import * as os from "node:os"
+import type { IStorage, SymbolIndex, DepsGraph } from "../../src/domain/services/IStorage.js"
+import type { ISessionStorage, SessionListItem } from "../../src/domain/services/ISessionStorage.js"
+import type { FileData } from "../../src/domain/value-objects/FileData.js"
+import type { FileAST } from "../../src/domain/value-objects/FileAST.js"
+import type { FileMeta } from "../../src/domain/value-objects/FileMeta.js"
+import type { UndoEntry } from "../../src/domain/value-objects/UndoEntry.js"
+import { Session } from "../../src/domain/entities/Session.js"
+import { ToolRegistry } from "../../src/infrastructure/tools/registry.js"
+import { OllamaClient } from "../../src/infrastructure/llm/OllamaClient.js"
+import { registerAllTools } from "../../src/cli/commands/tools-setup.js"
+import type { LLMConfig } from "../../src/shared/constants/config.js"
+
+/**
+ * Default LLM config for tests.
+ */
+export const DEFAULT_TEST_LLM_CONFIG: LLMConfig = {
+    model: "qwen2.5-coder:14b-instruct-q4_K_M",
+    contextWindow: 128_000,
+    temperature: 0.1,
+    host: "http://localhost:11434",
+    timeout: 180_000,
+    useNativeTools: true,
+}
+
+/**
+ * In-memory storage implementation for testing.
+ * Stores all data in Maps, no Redis required.
+ */
+export function createInMemoryStorage(): IStorage {
+    const files = new Map<string, FileData>()
+    const asts = new Map<string, FileAST>()
+    const metas = new Map<string, FileMeta>()
+    let symbolIndex: SymbolIndex = new Map()
+    let depsGraph: DepsGraph = { imports: new Map(), importedBy: new Map() }
+    const projectConfig = new Map<string, unknown>()
+    let connected = false
+
+    return {
+        getFile: vi.fn(async (filePath: string) => files.get(filePath) ?? null),
+        setFile: vi.fn(async (filePath: string, data: FileData) => {
+            files.set(filePath, data)
+        }),
+        deleteFile: vi.fn(async (filePath: string) => {
+            files.delete(filePath)
+        }),
+        getAllFiles: vi.fn(async () => new Map(files)),
+        getFileCount: vi.fn(async () => files.size),
+
+        getAST: vi.fn(async (filePath: string) => asts.get(filePath) ?? null),
+        setAST: vi.fn(async (filePath: string, ast: FileAST) => {
+            asts.set(filePath, ast)
+        }),
+        deleteAST: vi.fn(async (filePath: string) => {
+            asts.delete(filePath)
+        }),
+        getAllASTs: vi.fn(async () => new Map(asts)),
+
+        getMeta: vi.fn(async (filePath: string) => metas.get(filePath) ?? null),
+        setMeta: vi.fn(async (filePath: string, meta: FileMeta) => {
+            metas.set(filePath, meta)
+        }),
+        deleteMeta: vi.fn(async (filePath: string) => {
+            metas.delete(filePath)
+        }),
+        getAllMetas: vi.fn(async () => new Map(metas)),
+
+        getSymbolIndex: vi.fn(async () => symbolIndex),
+        setSymbolIndex: vi.fn(async (index: SymbolIndex) => {
+            symbolIndex = index
+        }),
+        getDepsGraph: vi.fn(async () => depsGraph),
+        setDepsGraph: vi.fn(async (graph: DepsGraph) => {
+            depsGraph = graph
+        }),
+
+        getProjectConfig: vi.fn(async (key: string) => projectConfig.get(key) ?? null),
+        setProjectConfig: vi.fn(async (key: string, value: unknown) => {
+            projectConfig.set(key, value)
+        }),
+
+        connect: vi.fn(async () => {
+            connected = true
+        }),
+        disconnect: vi.fn(async () => {
+            connected = false
+        }),
+        isConnected: vi.fn(() => connected),
+        clear: vi.fn(async () => {
+            files.clear()
+            asts.clear()
+            metas.clear()
+            symbolIndex = new Map()
+            depsGraph = { imports: new Map(), importedBy: new Map() }
+            projectConfig.clear()
+        }),
+    }
+}
+
+/**
+ * In-memory session storage for testing.
+ */
+export function createInMemorySessionStorage(): ISessionStorage {
+    const sessions = new Map<string, Session>()
+    const undoStacks = new Map<string, UndoEntry[]>()
+
+    return {
+        saveSession: vi.fn(async (session: Session) => {
+            sessions.set(session.id, session)
+        }),
+        loadSession: vi.fn(async (sessionId: string) => sessions.get(sessionId) ?? null),
+        deleteSession: vi.fn(async (sessionId: string) => {
+            sessions.delete(sessionId)
+            undoStacks.delete(sessionId)
+        }),
+        listSessions: vi.fn(async (projectName?: string): Promise<SessionListItem[]> => {
+            const items: SessionListItem[] = []
+            for (const session of sessions.values()) {
+                if (!projectName || session.projectName === projectName) {
+                    items.push({
+                        id: session.id,
+                        projectName: session.projectName,
+                        createdAt: session.createdAt,
+                        lastActivityAt: session.lastActivityAt,
+                        messageCount: session.history.length,
+                    })
+                }
+            }
+            return items
+        }),
+        getLatestSession: vi.fn(async (projectName: string) => {
+            let latest: Session | null = null
+            for (const session of sessions.values()) {
+                if (session.projectName === projectName) {
+                    if (!latest || session.lastActivityAt > latest.lastActivityAt) {
+                        latest = session
+                    }
+                }
+            }
+            return latest
+        }),
+        sessionExists: vi.fn(async (sessionId: string) => sessions.has(sessionId)),
+        pushUndoEntry: vi.fn(async (sessionId: string, entry: UndoEntry) => {
+            const stack = undoStacks.get(sessionId) ?? []
+            stack.push(entry)
+            undoStacks.set(sessionId, stack)
+        }),
+        popUndoEntry: vi.fn(async (sessionId: string) => {
+            const stack = undoStacks.get(sessionId) ?? []
+            return stack.pop() ?? null
+        }),
+        getUndoStack: vi.fn(async (sessionId: string) => undoStacks.get(sessionId) ?? []),
+        touchSession: vi.fn(async (sessionId: string) => {
+            const session = sessions.get(sessionId)
+            if (session) {
+                session.lastActivityAt = Date.now()
+            }
+        }),
+        clearAllSessions: vi.fn(async () => {
+            sessions.clear()
+            undoStacks.clear()
+        }),
+    }
+}
+
+/**
+ * Create REAL Ollama client for E2E tests.
+ */
+export function createRealOllamaClient(config?: Partial<LLMConfig>): OllamaClient {
+    return new OllamaClient({
+        ...DEFAULT_TEST_LLM_CONFIG,
+        ...config,
+    })
+}
+
+/**
+ * Create a tool registry with all 18 tools registered.
+ */
+export function createRealToolRegistry(): ToolRegistry {
+    const registry = new ToolRegistry()
+    registerAllTools(registry)
+    return registry
+}
+
+/**
+ * Create a new test session.
+ */
+export function createTestSession(projectName = "test-project"): Session {
+    return new Session(`test-${Date.now()}`, projectName)
+}
+
+/**
+ * Create a temporary test project directory with sample files.
+ */
+export async function createTestProject(): Promise<string> {
+    const tempDir = await fs.mkdtemp(path.join(os.tmpdir(), "ipuaro-e2e-"))
+
+    await fs.mkdir(path.join(tempDir, "src"), { recursive: true })
+
+    await fs.writeFile(
+        path.join(tempDir, "src", "index.ts"),
+        `/**
+ * Main entry point
+ */
+export function main(): void {
+    console.log("Hello, world!")
+}
+
+export function add(a: number, b: number): number {
+    return a + b
+}
+
+export function multiply(a: number, b: number): number {
+    return a * b
+}
+
+// TODO: Add more math functions
+main()
+`,
+    )
+
+    await fs.writeFile(
+        path.join(tempDir, "src", "utils.ts"),
+        `/**
+ * Utility functions
+ */
+import { add } from "./index.js"
+
+export function sum(numbers: number[]): number {
+    return numbers.reduce((acc, n) => add(acc, n), 0)
+}
+
+export class Calculator {
+    private result: number = 0
+
+    add(n: number): this {
+        this.result += n
+        return this
+    }
+
+    subtract(n: number): this {
+        this.result -= n
+        return this
+    }
+
+    getResult(): number {
+        return this.result
+    }
+
+    reset(): void {
+        this.result = 0
+    }
+}
+
+// FIXME: Handle edge cases for negative numbers
+`,
+    )
+
+    await fs.writeFile(
+        path.join(tempDir, "package.json"),
+        JSON.stringify(
+            {
+                name: "test-project",
+                version: "1.0.0",
+                type: "module",
+                scripts: {
+                    test: "echo 'Tests passed!'",
+                },
+            },
+            null,
+            4,
+        ),
+    )
+
+    await fs.writeFile(
+        path.join(tempDir, "README.md"),
+        `# Test Project
+
+A sample project for E2E testing.
+
+## Features
+- Basic math functions
+- Calculator class
+`,
+    )
+
+    return tempDir
+}
+
+/**
+ * Clean up test project directory.
+ */
+export async function cleanupTestProject(projectDir: string): Promise<void> {
+    await fs.rm(projectDir, { recursive: true, force: true })
+}
+
+/**
+ * All test dependencies bundled together.
+ */
+export interface E2ETestDependencies {
+    storage: IStorage
+    sessionStorage: ISessionStorage
+    llm: OllamaClient
+    tools: ToolRegistry
+    session: Session
+    projectRoot: string
+}
+
+/**
+ * Create all dependencies for E2E testing with REAL Ollama.
+ */
+export async function createE2ETestDependencies(
+    llmConfig?: Partial<LLMConfig>,
+): Promise<E2ETestDependencies> {
+    const projectRoot = await createTestProject()
+
+    return {
+        storage: createInMemoryStorage(),
+        sessionStorage: createInMemorySessionStorage(),
+        llm: createRealOllamaClient(llmConfig),
+        tools: createRealToolRegistry(),
+        session: createTestSession(),
+        projectRoot,
+    }
+}
+
+/**
+ * Check if Ollama is available.
+ */
+export async function isOllamaAvailable(): Promise<boolean> {
+    const client = createRealOllamaClient()
+    return client.isAvailable()
+}
+
+/**
+ * Check if required model is available.
+ */
+export async function isModelAvailable(
+    model = "qwen2.5-coder:14b-instruct-q4_K_M",
+): Promise<boolean> {
+    const client = createRealOllamaClient()
+    return client.hasModel(model)
+}

packages/ipuaro/tests/unit/application/use-cases/ContextManager.test.ts

@@ -245,4 +245,65 @@ describe("ContextManager", () => {
             expect(state.needsCompression).toBe(false)
         })
     })
+
+    describe("configuration", () => {
+        it("should use default compression threshold when no config provided", () => {
+            const manager = new ContextManager(CONTEXT_SIZE)
+            manager.addToContext("test.ts", CONTEXT_SIZE * 0.85)
+
+            expect(manager.needsCompression()).toBe(true)
+        })
+
+        it("should use custom compression threshold from config", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, { autoCompressAt: 0.9 })
+            manager.addToContext("test.ts", CONTEXT_SIZE * 0.85)
+
+            expect(manager.needsCompression()).toBe(false)
+        })
+
+        it("should trigger compression at custom threshold", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, { autoCompressAt: 0.9 })
+            manager.addToContext("test.ts", CONTEXT_SIZE * 0.95)
+
+            expect(manager.needsCompression()).toBe(true)
+        })
+
+        it("should accept compression method in config", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, { compressionMethod: "truncate" })
+
+            expect(manager).toBeDefined()
+        })
+
+        it("should use default compression method when not specified", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, {})
+
+            expect(manager).toBeDefined()
+        })
+
+        it("should accept full context config", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, {
+                systemPromptTokens: 3000,
+                maxContextUsage: 0.9,
+                autoCompressAt: 0.85,
+                compressionMethod: "llm-summary",
+            })
+
+            manager.addToContext("test.ts", CONTEXT_SIZE * 0.87)
+            expect(manager.needsCompression()).toBe(true)
+        })
+
+        it("should handle edge case: autoCompressAt = 0", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, { autoCompressAt: 0 })
+            manager.addToContext("test.ts", 1)
+
+            expect(manager.needsCompression()).toBe(true)
+        })
+
+        it("should handle edge case: autoCompressAt = 1", () => {
+            const manager = new ContextManager(CONTEXT_SIZE, { autoCompressAt: 1 })
+            manager.addToContext("test.ts", CONTEXT_SIZE * 0.99)
+
+            expect(manager.needsCompression()).toBe(false)
+        })
+    })
 })

packages/ipuaro/tests/unit/application/use-cases/HandleMessage.test.ts

@@ -198,12 +198,12 @@ describe("HandleMessage", () => {
             expect(toolMessages.length).toBeGreaterThan(0)
         })
 
-        it("should return error for unknown tools", async () => {
+        it("should return error for unregistered tools", async () => {
             vi.mocked(mockTools.get).mockReturnValue(undefined)
             vi.mocked(mockLLM.chat)
                 .mockResolvedValueOnce(
                     createMockLLMResponse(
-                        '<tool_call name="unknown_tool"><param>value</param></tool_call>',
+                        '<tool_call name="get_complexity"><path>src</path></tool_call>',
                         true,
                     ),
                 )

packages/ipuaro/tests/unit/application/use-cases/IndexProject.test.ts

@@ -0,0 +1,318 @@
+import { describe, it, expect, vi, beforeEach } from "vitest"
+import { IndexProject } from "../../../../src/application/use-cases/IndexProject.js"
+import type { IStorage, SymbolIndex, DepsGraph } from "../../../../src/domain/services/IStorage.js"
+import type { IndexProgress } from "../../../../src/domain/services/IIndexer.js"
+import { createFileData } from "../../../../src/domain/value-objects/FileData.js"
+import { createEmptyFileAST } from "../../../../src/domain/value-objects/FileAST.js"
+import { createFileMeta } from "../../../../src/domain/value-objects/FileMeta.js"
+
+vi.mock("../../../../src/infrastructure/indexer/FileScanner.js", () => ({
+    FileScanner: class {
+        async scanAll() {
+            return [
+                { path: "src/index.ts", type: "file", size: 100, lastModified: Date.now() },
+                { path: "src/utils.ts", type: "file", size: 200, lastModified: Date.now() },
+            ]
+        }
+        static async readFileContent(path: string) {
+            if (path.includes("index.ts")) {
+                return 'export function main() { return "hello" }'
+            }
+            if (path.includes("utils.ts")) {
+                return "export const add = (a: number, b: number) => a + b"
+            }
+            return null
+        }
+    },
+}))
+
+vi.mock("../../../../src/infrastructure/indexer/ASTParser.js", () => ({
+    ASTParser: class {
+        parse() {
+            return {
+                ...createEmptyFileAST(),
+                functions: [
+                    {
+                        name: "test",
+                        lineStart: 1,
+                        lineEnd: 5,
+                        params: [],
+                        isAsync: false,
+                        isExported: true,
+                    },
+                ],
+            }
+        }
+    },
+}))
+
+vi.mock("../../../../src/infrastructure/indexer/MetaAnalyzer.js", () => ({
+    MetaAnalyzer: class {
+        constructor() {}
+        analyze() {
+            return createFileMeta()
+        }
+    },
+}))
+
+vi.mock("../../../../src/infrastructure/indexer/IndexBuilder.js", () => ({
+    IndexBuilder: class {
+        constructor() {}
+        buildSymbolIndex() {
+            return new Map([
+                ["test", [{ path: "src/index.ts", line: 1, type: "function" }]],
+            ]) as SymbolIndex
+        }
+        buildDepsGraph() {
+            return {
+                imports: new Map(),
+                importedBy: new Map(),
+            } as DepsGraph
+        }
+    },
+}))
+
+describe("IndexProject", () => {
+    let useCase: IndexProject
+    let mockStorage: IStorage
+
+    beforeEach(() => {
+        mockStorage = {
+            getFile: vi.fn().mockResolvedValue(null),
+            setFile: vi.fn().mockResolvedValue(undefined),
+            deleteFile: vi.fn().mockResolvedValue(undefined),
+            getAllFiles: vi.fn().mockResolvedValue(new Map()),
+            getFileCount: vi.fn().mockResolvedValue(0),
+            getAST: vi.fn().mockResolvedValue(null),
+            setAST: vi.fn().mockResolvedValue(undefined),
+            deleteAST: vi.fn().mockResolvedValue(undefined),
+            getAllASTs: vi.fn().mockResolvedValue(new Map()),
+            getMeta: vi.fn().mockResolvedValue(null),
+            setMeta: vi.fn().mockResolvedValue(undefined),
+            deleteMeta: vi.fn().mockResolvedValue(undefined),
+            getAllMetas: vi.fn().mockResolvedValue(new Map()),
+            getSymbolIndex: vi.fn().mockResolvedValue(new Map()),
+            setSymbolIndex: vi.fn().mockResolvedValue(undefined),
+            getDepsGraph: vi.fn().mockResolvedValue({ imports: new Map(), importedBy: new Map() }),
+            setDepsGraph: vi.fn().mockResolvedValue(undefined),
+            getProjectConfig: vi.fn().mockResolvedValue(null),
+            setProjectConfig: vi.fn().mockResolvedValue(undefined),
+            connect: vi.fn().mockResolvedValue(undefined),
+            disconnect: vi.fn().mockResolvedValue(undefined),
+            isConnected: vi.fn().mockReturnValue(true),
+            clear: vi.fn().mockResolvedValue(undefined),
+        }
+
+        useCase = new IndexProject(mockStorage, "/test/project")
+    })
+
+    describe("execute", () => {
+        it("should index project and return stats", async () => {
+            const stats = await useCase.execute("/test/project")
+
+            expect(stats.filesScanned).toBe(2)
+            expect(stats.filesParsed).toBe(2)
+            expect(stats.parseErrors).toBe(0)
+            expect(stats.timeMs).toBeGreaterThanOrEqual(0)
+        })
+
+        it("should store file data for all scanned files", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setFile).toHaveBeenCalledTimes(2)
+            expect(mockStorage.setFile).toHaveBeenCalledWith(
+                "src/index.ts",
+                expect.objectContaining({
+                    hash: expect.any(String),
+                    lines: expect.any(Array),
+                }),
+            )
+        })
+
+        it("should store AST for all parsed files", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setAST).toHaveBeenCalledTimes(2)
+            expect(mockStorage.setAST).toHaveBeenCalledWith(
+                "src/index.ts",
+                expect.objectContaining({
+                    functions: expect.any(Array),
+                }),
+            )
+        })
+
+        it("should store metadata for all files", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setMeta).toHaveBeenCalledTimes(2)
+            expect(mockStorage.setMeta).toHaveBeenCalledWith("src/index.ts", expect.any(Object))
+        })
+
+        it("should build and store symbol index", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setSymbolIndex).toHaveBeenCalledTimes(1)
+            expect(mockStorage.setSymbolIndex).toHaveBeenCalledWith(expect.any(Map))
+        })
+
+        it("should build and store dependency graph", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setDepsGraph).toHaveBeenCalledTimes(1)
+            expect(mockStorage.setDepsGraph).toHaveBeenCalledWith(
+                expect.objectContaining({
+                    imports: expect.any(Map),
+                    importedBy: expect.any(Map),
+                }),
+            )
+        })
+
+        it("should store last indexed timestamp", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setProjectConfig).toHaveBeenCalledWith(
+                "last_indexed",
+                expect.any(Number),
+            )
+        })
+
+        it("should call progress callback during indexing", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            expect(progressCallback).toHaveBeenCalled()
+            expect(progressCallback).toHaveBeenCalledWith(
+                expect.objectContaining({
+                    current: expect.any(Number),
+                    total: expect.any(Number),
+                    currentFile: expect.any(String),
+                    phase: expect.stringMatching(/scanning|parsing|analyzing|indexing/),
+                }),
+            )
+        })
+
+        it("should report scanning phase", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const scanningCalls = progressCallback.mock.calls.filter(
+                (call) => call[0].phase === "scanning",
+            )
+            expect(scanningCalls.length).toBeGreaterThan(0)
+        })
+
+        it("should report parsing phase", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const parsingCalls = progressCallback.mock.calls.filter(
+                (call) => call[0].phase === "parsing",
+            )
+            expect(parsingCalls.length).toBeGreaterThan(0)
+        })
+
+        it("should report analyzing phase", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const analyzingCalls = progressCallback.mock.calls.filter(
+                (call) => call[0].phase === "analyzing",
+            )
+            expect(analyzingCalls.length).toBeGreaterThan(0)
+        })
+
+        it("should report indexing phase", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const indexingCalls = progressCallback.mock.calls.filter(
+                (call) => call[0].phase === "indexing",
+            )
+            expect(indexingCalls.length).toBeGreaterThan(0)
+        })
+
+        it("should detect TypeScript files", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setAST).toHaveBeenCalledWith("src/index.ts", expect.any(Object))
+        })
+
+        it("should handle files without parseable language", async () => {
+            vi.mocked(mockStorage.setFile).mockClear()
+
+            await useCase.execute("/test/project")
+
+            const stats = await useCase.execute("/test/project")
+            expect(stats.filesScanned).toBeGreaterThanOrEqual(0)
+        })
+
+        it("should calculate indexing duration", async () => {
+            const startTime = Date.now()
+            const stats = await useCase.execute("/test/project")
+            const endTime = Date.now()
+
+            expect(stats.timeMs).toBeGreaterThanOrEqual(0)
+            expect(stats.timeMs).toBeLessThanOrEqual(endTime - startTime + 10)
+        })
+    })
+
+    describe("language detection", () => {
+        it("should detect .ts files", async () => {
+            await useCase.execute("/test/project")
+
+            expect(mockStorage.setAST).toHaveBeenCalledWith(
+                expect.stringContaining(".ts"),
+                expect.any(Object),
+            )
+        })
+    })
+
+    describe("progress reporting", () => {
+        it("should not fail if progress callback is not provided", async () => {
+            await expect(useCase.execute("/test/project")).resolves.toBeDefined()
+        })
+
+        it("should include current file in progress updates", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const callsWithFiles = progressCallback.mock.calls.filter(
+                (call) => call[0].currentFile && call[0].currentFile.length > 0,
+            )
+            expect(callsWithFiles.length).toBeGreaterThan(0)
+        })
+
+        it("should report correct total count", async () => {
+            const progressCallback = vi.fn()
+
+            await useCase.execute("/test/project", {
+                onProgress: progressCallback,
+            })
+
+            const parsingCalls = progressCallback.mock.calls.filter(
+                (call) => call[0].phase === "parsing",
+            )
+            if (parsingCalls.length > 0) {
+                expect(parsingCalls[0][0].total).toBe(2)
+            }
+        })
+    })
+})

packages/ipuaro/tests/unit/cli/commands/init.test.ts

@@ -0,0 +1,117 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from "vitest"
+import * as fs from "node:fs/promises"
+import * as path from "node:path"
+import { executeInit } from "../../../../src/cli/commands/init.js"
+
+vi.mock("node:fs/promises")
+
+describe("executeInit", () => {
+    const testPath = "/test/project"
+    const configPath = path.join(testPath, ".ipuaro.json")
+
+    beforeEach(() => {
+        vi.clearAllMocks()
+        vi.spyOn(console, "warn").mockImplementation(() => {})
+        vi.spyOn(console, "error").mockImplementation(() => {})
+    })
+
+    afterEach(() => {
+        vi.restoreAllMocks()
+    })
+
+    it("should create .ipuaro.json file successfully", async () => {
+        vi.mocked(fs.access).mockRejectedValue(new Error("ENOENT"))
+        vi.mocked(fs.mkdir).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockResolvedValue(undefined)
+
+        const result = await executeInit(testPath)
+
+        expect(result.success).toBe(true)
+        expect(result.filePath).toBe(configPath)
+        expect(fs.writeFile).toHaveBeenCalledWith(
+            configPath,
+            expect.stringContaining('"redis"'),
+            "utf-8",
+        )
+    })
+
+    it("should skip existing file without force option", async () => {
+        vi.mocked(fs.access).mockResolvedValue(undefined)
+
+        const result = await executeInit(testPath)
+
+        expect(result.success).toBe(true)
+        expect(result.skipped).toBe(true)
+        expect(fs.writeFile).not.toHaveBeenCalled()
+    })
+
+    it("should overwrite existing file with force option", async () => {
+        vi.mocked(fs.access).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockResolvedValue(undefined)
+
+        const result = await executeInit(testPath, { force: true })
+
+        expect(result.success).toBe(true)
+        expect(result.skipped).toBeUndefined()
+        expect(fs.writeFile).toHaveBeenCalled()
+    })
+
+    it("should handle write errors", async () => {
+        vi.mocked(fs.access).mockRejectedValue(new Error("ENOENT"))
+        vi.mocked(fs.mkdir).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockRejectedValue(new Error("Permission denied"))
+
+        const result = await executeInit(testPath)
+
+        expect(result.success).toBe(false)
+        expect(result.error).toContain("Permission denied")
+    })
+
+    it("should create parent directories if needed", async () => {
+        vi.mocked(fs.access)
+            .mockRejectedValueOnce(new Error("ENOENT"))
+            .mockRejectedValueOnce(new Error("ENOENT"))
+        vi.mocked(fs.mkdir).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockResolvedValue(undefined)
+
+        const result = await executeInit(testPath)
+
+        expect(result.success).toBe(true)
+        expect(fs.mkdir).toHaveBeenCalledWith(expect.any(String), { recursive: true })
+    })
+
+    it("should use current directory as default", async () => {
+        vi.mocked(fs.access).mockRejectedValue(new Error("ENOENT"))
+        vi.mocked(fs.mkdir).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockResolvedValue(undefined)
+
+        const result = await executeInit()
+
+        expect(result.success).toBe(true)
+        expect(result.filePath).toContain(".ipuaro.json")
+    })
+
+    it("should include expected config sections", async () => {
+        vi.mocked(fs.access).mockRejectedValue(new Error("ENOENT"))
+        vi.mocked(fs.mkdir).mockResolvedValue(undefined)
+        vi.mocked(fs.writeFile).mockResolvedValue(undefined)
+
+        await executeInit(testPath)
+
+        const writeCall = vi.mocked(fs.writeFile).mock.calls[0]
+        const content = writeCall[1] as string
+        const config = JSON.parse(content) as {
+            redis: unknown
+            llm: unknown
+            edit: unknown
+        }
+
+        expect(config).toHaveProperty("redis")
+        expect(config).toHaveProperty("llm")
+        expect(config).toHaveProperty("edit")
+        expect(config.redis).toHaveProperty("host", "localhost")
+        expect(config.redis).toHaveProperty("port", 6379)
+        expect(config.llm).toHaveProperty("model", "qwen2.5-coder:7b-instruct")
+        expect(config.edit).toHaveProperty("autoApply", false)
+    })
+})

packages/ipuaro/tests/unit/cli/commands/onboarding.test.ts

@@ -0,0 +1,353 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from "vitest"
+import {
+    checkRedis,
+    checkOllama,
+    checkModel,
+    checkProjectSize,
+    runOnboarding,
+} from "../../../../src/cli/commands/onboarding.js"
+import { RedisClient } from "../../../../src/infrastructure/storage/RedisClient.js"
+import { OllamaClient } from "../../../../src/infrastructure/llm/OllamaClient.js"
+import { FileScanner } from "../../../../src/infrastructure/indexer/FileScanner.js"
+
+vi.mock("../../../../src/infrastructure/storage/RedisClient.js")
+vi.mock("../../../../src/infrastructure/llm/OllamaClient.js")
+vi.mock("../../../../src/infrastructure/indexer/FileScanner.js")
+
+describe("onboarding", () => {
+    beforeEach(() => {
+        vi.clearAllMocks()
+    })
+
+    afterEach(() => {
+        vi.restoreAllMocks()
+    })
+
+    describe("checkRedis", () => {
+        it("should return ok when Redis connects and pings successfully", async () => {
+            const mockConnect = vi.fn().mockResolvedValue(undefined)
+            const mockPing = vi.fn().mockResolvedValue(true)
+            const mockDisconnect = vi.fn().mockResolvedValue(undefined)
+
+            vi.mocked(RedisClient).mockImplementation(
+                () =>
+                    ({
+                        connect: mockConnect,
+                        ping: mockPing,
+                        disconnect: mockDisconnect,
+                    }) as unknown as RedisClient,
+            )
+
+            const result = await checkRedis({
+                host: "localhost",
+                port: 6379,
+                db: 0,
+                keyPrefix: "ipuaro:",
+            })
+
+            expect(result.ok).toBe(true)
+            expect(result.error).toBeUndefined()
+            expect(mockConnect).toHaveBeenCalled()
+            expect(mockPing).toHaveBeenCalled()
+            expect(mockDisconnect).toHaveBeenCalled()
+        })
+
+        it("should return error when Redis connection fails", async () => {
+            vi.mocked(RedisClient).mockImplementation(
+                () =>
+                    ({
+                        connect: vi.fn().mockRejectedValue(new Error("Connection refused")),
+                    }) as unknown as RedisClient,
+            )
+
+            const result = await checkRedis({
+                host: "localhost",
+                port: 6379,
+                db: 0,
+                keyPrefix: "ipuaro:",
+            })
+
+            expect(result.ok).toBe(false)
+            expect(result.error).toContain("Cannot connect to Redis")
+        })
+
+        it("should return error when ping fails", async () => {
+            vi.mocked(RedisClient).mockImplementation(
+                () =>
+                    ({
+                        connect: vi.fn().mockResolvedValue(undefined),
+                        ping: vi.fn().mockResolvedValue(false),
+                        disconnect: vi.fn().mockResolvedValue(undefined),
+                    }) as unknown as RedisClient,
+            )
+
+            const result = await checkRedis({
+                host: "localhost",
+                port: 6379,
+                db: 0,
+                keyPrefix: "ipuaro:",
+            })
+
+            expect(result.ok).toBe(false)
+            expect(result.error).toContain("Redis ping failed")
+        })
+    })
+
+    describe("checkOllama", () => {
+        it("should return ok when Ollama is available", async () => {
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        isAvailable: vi.fn().mockResolvedValue(true),
+                    }) as unknown as OllamaClient,
+            )
+
+            const result = await checkOllama({
+                model: "qwen2.5-coder:7b-instruct",
+                contextWindow: 128_000,
+                temperature: 0.1,
+                host: "http://localhost:11434",
+                timeout: 120_000,
+            })
+
+            expect(result.ok).toBe(true)
+            expect(result.error).toBeUndefined()
+        })
+
+        it("should return error when Ollama is not available", async () => {
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        isAvailable: vi.fn().mockResolvedValue(false),
+                    }) as unknown as OllamaClient,
+            )
+
+            const result = await checkOllama({
+                model: "qwen2.5-coder:7b-instruct",
+                contextWindow: 128_000,
+                temperature: 0.1,
+                host: "http://localhost:11434",
+                timeout: 120_000,
+            })
+
+            expect(result.ok).toBe(false)
+            expect(result.error).toContain("Cannot connect to Ollama")
+        })
+    })
+
+    describe("checkModel", () => {
+        it("should return ok when model is available", async () => {
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        hasModel: vi.fn().mockResolvedValue(true),
+                    }) as unknown as OllamaClient,
+            )
+
+            const result = await checkModel({
+                model: "qwen2.5-coder:7b-instruct",
+                contextWindow: 128_000,
+                temperature: 0.1,
+                host: "http://localhost:11434",
+                timeout: 120_000,
+            })
+
+            expect(result.ok).toBe(true)
+            expect(result.needsPull).toBe(false)
+        })
+
+        it("should return needsPull when model is not available", async () => {
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        hasModel: vi.fn().mockResolvedValue(false),
+                    }) as unknown as OllamaClient,
+            )
+
+            const result = await checkModel({
+                model: "qwen2.5-coder:7b-instruct",
+                contextWindow: 128_000,
+                temperature: 0.1,
+                host: "http://localhost:11434",
+                timeout: 120_000,
+            })
+
+            expect(result.ok).toBe(false)
+            expect(result.needsPull).toBe(true)
+            expect(result.error).toContain("not installed")
+        })
+    })
+
+    describe("checkProjectSize", () => {
+        it("should return ok when file count is within limits", async () => {
+            vi.mocked(FileScanner).mockImplementation(
+                () =>
+                    ({
+                        scanAll: vi.fn().mockResolvedValue(
+                            Array.from({ length: 100 }, (_, i) => ({
+                                path: `file${String(i)}.ts`,
+                                type: "file" as const,
+                                size: 1000,
+                                lastModified: Date.now(),
+                            })),
+                        ),
+                    }) as unknown as FileScanner,
+            )
+
+            const result = await checkProjectSize("/test/path")
+
+            expect(result.ok).toBe(true)
+            expect(result.fileCount).toBe(100)
+            expect(result.warning).toBeUndefined()
+        })
+
+        it("should return warning when file count exceeds limit", async () => {
+            vi.mocked(FileScanner).mockImplementation(
+                () =>
+                    ({
+                        scanAll: vi.fn().mockResolvedValue(
+                            Array.from({ length: 15000 }, (_, i) => ({
+                                path: `file${String(i)}.ts`,
+                                type: "file" as const,
+                                size: 1000,
+                                lastModified: Date.now(),
+                            })),
+                        ),
+                    }) as unknown as FileScanner,
+            )
+
+            const result = await checkProjectSize("/test/path", 10_000)
+
+            expect(result.ok).toBe(true)
+            expect(result.fileCount).toBe(15000)
+            expect(result.warning).toContain("15")
+            expect(result.warning).toContain("000 files")
+        })
+
+        it("should return error when no files found", async () => {
+            vi.mocked(FileScanner).mockImplementation(
+                () =>
+                    ({
+                        scanAll: vi.fn().mockResolvedValue([]),
+                    }) as unknown as FileScanner,
+            )
+
+            const result = await checkProjectSize("/test/path")
+
+            expect(result.ok).toBe(false)
+            expect(result.fileCount).toBe(0)
+            expect(result.warning).toContain("No supported files found")
+        })
+    })
+
+    describe("runOnboarding", () => {
+        it("should return success when all checks pass", async () => {
+            vi.mocked(RedisClient).mockImplementation(
+                () =>
+                    ({
+                        connect: vi.fn().mockResolvedValue(undefined),
+                        ping: vi.fn().mockResolvedValue(true),
+                        disconnect: vi.fn().mockResolvedValue(undefined),
+                    }) as unknown as RedisClient,
+            )
+
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        isAvailable: vi.fn().mockResolvedValue(true),
+                        hasModel: vi.fn().mockResolvedValue(true),
+                    }) as unknown as OllamaClient,
+            )
+
+            vi.mocked(FileScanner).mockImplementation(
+                () =>
+                    ({
+                        scanAll: vi.fn().mockResolvedValue([{ path: "file.ts" }]),
+                    }) as unknown as FileScanner,
+            )
+
+            const result = await runOnboarding({
+                redisConfig: { host: "localhost", port: 6379, db: 0, keyPrefix: "ipuaro:" },
+                llmConfig: {
+                    model: "test",
+                    contextWindow: 128_000,
+                    temperature: 0.1,
+                    host: "http://localhost:11434",
+                    timeout: 120_000,
+                },
+                projectPath: "/test/path",
+            })
+
+            expect(result.success).toBe(true)
+            expect(result.redisOk).toBe(true)
+            expect(result.ollamaOk).toBe(true)
+            expect(result.modelOk).toBe(true)
+            expect(result.projectOk).toBe(true)
+            expect(result.errors).toHaveLength(0)
+        })
+
+        it("should return failure when Redis fails", async () => {
+            vi.mocked(RedisClient).mockImplementation(
+                () =>
+                    ({
+                        connect: vi.fn().mockRejectedValue(new Error("Connection refused")),
+                    }) as unknown as RedisClient,
+            )
+
+            vi.mocked(OllamaClient).mockImplementation(
+                () =>
+                    ({
+                        isAvailable: vi.fn().mockResolvedValue(true),
+                        hasModel: vi.fn().mockResolvedValue(true),
+                    }) as unknown as OllamaClient,
+            )
+
+            vi.mocked(FileScanner).mockImplementation(
+                () =>
+                    ({
+                        scanAll: vi.fn().mockResolvedValue([{ path: "file.ts" }]),
+                    }) as unknown as FileScanner,
+            )
+
+            const result = await runOnboarding({
+                redisConfig: { host: "localhost", port: 6379, db: 0, keyPrefix: "ipuaro:" },
+                llmConfig: {
+                    model: "test",
+                    contextWindow: 128_000,
+                    temperature: 0.1,
+                    host: "http://localhost:11434",
+                    timeout: 120_000,
+                },
+                projectPath: "/test/path",
+            })
+
+            expect(result.success).toBe(false)
+            expect(result.redisOk).toBe(false)
+            expect(result.errors.length).toBeGreaterThan(0)
+        })
+
+        it("should skip checks when skip options are set", async () => {
+            const result = await runOnboarding({
+                redisConfig: { host: "localhost", port: 6379, db: 0, keyPrefix: "ipuaro:" },
+                llmConfig: {
+                    model: "test",
+                    contextWindow: 128_000,
+                    temperature: 0.1,
+                    host: "http://localhost:11434",
+                    timeout: 120_000,
+                },
+                projectPath: "/test/path",
+                skipRedis: true,
+                skipOllama: true,
+                skipModel: true,
+                skipProject: true,
+            })
+
+            expect(result.success).toBe(true)
+            expect(result.redisOk).toBe(true)
+            expect(result.ollamaOk).toBe(true)
+            expect(result.modelOk).toBe(true)
+            expect(result.projectOk).toBe(true)
+        })
+    })
+})

packages/ipuaro/tests/unit/cli/commands/tools-setup.test.ts

@@ -0,0 +1,111 @@
+import { describe, it, expect } from "vitest"
+import { registerAllTools } from "../../../../src/cli/commands/tools-setup.js"
+import { ToolRegistry } from "../../../../src/infrastructure/tools/registry.js"
+
+describe("registerAllTools", () => {
+    it("should register all 18 tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.size).toBe(18)
+    })
+
+    it("should register all read tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("get_lines")).toBe(true)
+        expect(registry.has("get_function")).toBe(true)
+        expect(registry.has("get_class")).toBe(true)
+        expect(registry.has("get_structure")).toBe(true)
+    })
+
+    it("should register all edit tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("edit_lines")).toBe(true)
+        expect(registry.has("create_file")).toBe(true)
+        expect(registry.has("delete_file")).toBe(true)
+    })
+
+    it("should register all search tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("find_references")).toBe(true)
+        expect(registry.has("find_definition")).toBe(true)
+    })
+
+    it("should register all analysis tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("get_dependencies")).toBe(true)
+        expect(registry.has("get_dependents")).toBe(true)
+        expect(registry.has("get_complexity")).toBe(true)
+        expect(registry.has("get_todos")).toBe(true)
+    })
+
+    it("should register all git tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("git_status")).toBe(true)
+        expect(registry.has("git_diff")).toBe(true)
+        expect(registry.has("git_commit")).toBe(true)
+    })
+
+    it("should register all run tools", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        expect(registry.has("run_command")).toBe(true)
+        expect(registry.has("run_tests")).toBe(true)
+    })
+
+    it("should register tools with correct categories", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        const readTools = registry.getByCategory("read")
+        const editTools = registry.getByCategory("edit")
+        const searchTools = registry.getByCategory("search")
+        const analysisTools = registry.getByCategory("analysis")
+        const gitTools = registry.getByCategory("git")
+        const runTools = registry.getByCategory("run")
+
+        expect(readTools.length).toBe(4)
+        expect(editTools.length).toBe(3)
+        expect(searchTools.length).toBe(2)
+        expect(analysisTools.length).toBe(4)
+        expect(gitTools.length).toBe(3)
+        expect(runTools.length).toBe(2)
+    })
+
+    it("should register tools with requiresConfirmation flag", () => {
+        const registry = new ToolRegistry()
+
+        registerAllTools(registry)
+
+        const confirmationTools = registry.getConfirmationTools()
+        const safeTools = registry.getSafeTools()
+
+        expect(confirmationTools.length).toBeGreaterThan(0)
+        expect(safeTools.length).toBeGreaterThan(0)
+
+        const confirmNames = confirmationTools.map((t) => t.name)
+        expect(confirmNames).toContain("edit_lines")
+        expect(confirmNames).toContain("create_file")
+        expect(confirmNames).toContain("delete_file")
+        expect(confirmNames).toContain("git_commit")
+    })
+})

packages/ipuaro/tests/unit/domain/value-objects/FileMeta.test.ts

@@ -1,5 +1,9 @@
 import { describe, it, expect } from "vitest"
-import { createFileMeta, isHubFile } from "../../../../src/domain/value-objects/FileMeta.js"
+import {
+    calculateImpactScore,
+    createFileMeta,
+    isHubFile,
+} from "../../../../src/domain/value-objects/FileMeta.js"
 
 describe("FileMeta", () => {
     describe("createFileMeta", () => {
@@ -15,6 +19,7 @@ describe("FileMeta", () => {
             expect(meta.isHub).toBe(false)
             expect(meta.isEntryPoint).toBe(false)
             expect(meta.fileType).toBe("unknown")
+            expect(meta.impactScore).toBe(0)
         })
 
         it("should merge partial values", () => {
@@ -42,4 +47,51 @@ describe("FileMeta", () => {
             expect(isHubFile(0)).toBe(false)
         })
     })
+
+    describe("calculateImpactScore", () => {
+        it("should return 0 for file with 0 dependents", () => {
+            expect(calculateImpactScore(0, 10)).toBe(0)
+        })
+
+        it("should return 0 when totalFiles is 0", () => {
+            expect(calculateImpactScore(5, 0)).toBe(0)
+        })
+
+        it("should return 0 when totalFiles is 1", () => {
+            expect(calculateImpactScore(0, 1)).toBe(0)
+        })
+
+        it("should calculate correct percentage", () => {
+            // 5 dependents out of 10 files (excluding itself = 9 possible)
+            // 5/9 * 100 = 55.56 → rounded to 56
+            expect(calculateImpactScore(5, 10)).toBe(56)
+        })
+
+        it("should return 100 when all other files depend on it", () => {
+            // 9 dependents out of 10 files (9 possible dependents)
+            expect(calculateImpactScore(9, 10)).toBe(100)
+        })
+
+        it("should cap at 100", () => {
+            // Edge case: more dependents than possible (shouldn't happen normally)
+            expect(calculateImpactScore(20, 10)).toBe(100)
+        })
+
+        it("should round the percentage", () => {
+            // 1 dependent out of 3 files (2 possible)
+            // 1/2 * 100 = 50
+            expect(calculateImpactScore(1, 3)).toBe(50)
+        })
+
+        it("should calculate impact for small projects", () => {
+            // 1 dependent out of 2 files (1 possible)
+            expect(calculateImpactScore(1, 2)).toBe(100)
+        })
+
+        it("should calculate impact for larger projects", () => {
+            // 50 dependents out of 100 files (99 possible)
+            // 50/99 * 100 = 50.51 → rounded to 51
+            expect(calculateImpactScore(50, 100)).toBe(51)
+        })
+    })
 })

packages/ipuaro/tests/unit/infrastructure/indexer/ASTParser.test.ts

@@ -224,6 +224,62 @@ describe("ASTParser", () => {
             const ast = parser.parse(code, "ts")
             expect(ast.typeAliases[0].isExported).toBe(true)
         })
+
+        it("should extract type alias definition (simple)", () => {
+            const code = `type UserId = string`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("string")
+        })
+
+        it("should extract type alias definition (union)", () => {
+            const code = `type Status = "pending" | "active" | "done"`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe('"pending" | "active" | "done"')
+        })
+
+        it("should extract type alias definition (intersection)", () => {
+            const code = `type AdminUser = User & Admin`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("User & Admin")
+        })
+
+        it("should extract type alias definition (object type)", () => {
+            const code = `type Point = { x: number; y: number }`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("{ x: number; y: number }")
+        })
+
+        it("should extract type alias definition (function type)", () => {
+            const code = `type Handler = (event: Event) => void`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("(event: Event) => void")
+        })
+
+        it("should extract type alias definition (generic)", () => {
+            const code = `type Result<T> = { success: boolean; data: T }`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("{ success: boolean; data: T }")
+        })
+
+        it("should extract type alias definition (array)", () => {
+            const code = `type UserIds = string[]`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("string[]")
+        })
+
+        it("should extract type alias definition (tuple)", () => {
+            const code = `type Pair = [string, number]`
+            const ast = parser.parse(code, "ts")
+            expect(ast.typeAliases).toHaveLength(1)
+            expect(ast.typeAliases[0].definition).toBe("[string, number]")
+        })
     })
 
     describe("exports", () => {
@@ -404,4 +460,376 @@ function mix(
             expect(ast.exports.length).toBeGreaterThanOrEqual(4)
         })
     })
+
+    describe("JSON parsing", () => {
+        it("should extract top-level keys from JSON object", () => {
+            const json = `{
+    "name": "test",
+    "version": "1.0.0",
+    "dependencies": {},
+    "scripts": {}
+}`
+            const ast = parser.parse(json, "json")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(4)
+            expect(ast.exports.map((e) => e.name)).toEqual([
+                "name",
+                "version",
+                "dependencies",
+                "scripts",
+            ])
+            expect(ast.exports.every((e) => e.kind === "variable")).toBe(true)
+        })
+
+        it("should handle empty JSON object", () => {
+            const json = `{}`
+            const ast = parser.parse(json, "json")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(0)
+        })
+    })
+
+    describe("YAML parsing", () => {
+        it("should extract top-level keys from YAML", () => {
+            const yaml = `name: test
+version: 1.0.0
+dependencies:
+  foo: ^1.0.0
+scripts:
+  test: vitest`
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports.length).toBeGreaterThanOrEqual(4)
+            expect(ast.exports.map((e) => e.name)).toContain("name")
+            expect(ast.exports.map((e) => e.name)).toContain("version")
+            expect(ast.exports.every((e) => e.kind === "variable")).toBe(true)
+        })
+
+        it("should handle YAML array at root", () => {
+            const yaml = `- item1
+- item2
+- item3`
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(1)
+            expect(ast.exports[0].name).toBe("(array)")
+        })
+
+        it("should handle empty YAML", () => {
+            const yaml = ``
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(0)
+        })
+
+        it("should handle YAML with null content", () => {
+            const yaml = `null`
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(0)
+        })
+
+        it("should handle invalid YAML with parse error", () => {
+            const yaml = `{invalid: yaml: syntax: [}`
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(true)
+            expect(ast.parseErrorMessage).toBeDefined()
+        })
+
+        it("should track correct line numbers for YAML keys", () => {
+            const yaml = `first: value1
+second: value2
+third: value3`
+
+            const ast = parser.parse(yaml, "yaml")
+
+            expect(ast.parseError).toBe(false)
+            expect(ast.exports).toHaveLength(3)
+            expect(ast.exports[0].line).toBe(1)
+            expect(ast.exports[1].line).toBe(2)
+            expect(ast.exports[2].line).toBe(3)
+        })
+    })
+
+    describe("enums (0.24.3)", () => {
+        it("should extract enum with numeric values", () => {
+            const code = `enum Status {
+                Active = 1,
+                Inactive = 0,
+                Pending = 2
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0]).toMatchObject({
+                name: "Status",
+                isExported: false,
+                isConst: false,
+            })
+            expect(ast.enums[0].members).toHaveLength(3)
+            expect(ast.enums[0].members[0]).toMatchObject({ name: "Active", value: 1 })
+            expect(ast.enums[0].members[1]).toMatchObject({ name: "Inactive", value: 0 })
+            expect(ast.enums[0].members[2]).toMatchObject({ name: "Pending", value: 2 })
+        })
+
+        it("should extract enum with string values", () => {
+            const code = `enum Role {
+                Admin = "admin",
+                User = "user",
+                Guest = "guest"
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].members).toHaveLength(3)
+            expect(ast.enums[0].members[0]).toMatchObject({ name: "Admin", value: "admin" })
+            expect(ast.enums[0].members[1]).toMatchObject({ name: "User", value: "user" })
+            expect(ast.enums[0].members[2]).toMatchObject({ name: "Guest", value: "guest" })
+        })
+
+        it("should extract enum without explicit values", () => {
+            const code = `enum Direction {
+                Up,
+                Down,
+                Left,
+                Right
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].members).toHaveLength(4)
+            expect(ast.enums[0].members[0]).toMatchObject({ name: "Up", value: undefined })
+            expect(ast.enums[0].members[1]).toMatchObject({ name: "Down", value: undefined })
+        })
+
+        it("should extract exported enum", () => {
+            const code = `export enum Color {
+                Red = "#FF0000",
+                Green = "#00FF00",
+                Blue = "#0000FF"
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].isExported).toBe(true)
+            expect(ast.exports).toHaveLength(1)
+            expect(ast.exports[0].kind).toBe("type")
+        })
+
+        it("should extract const enum", () => {
+            const code = `const enum HttpStatus {
+                OK = 200,
+                NotFound = 404,
+                InternalError = 500
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].isConst).toBe(true)
+            expect(ast.enums[0].members[0]).toMatchObject({ name: "OK", value: 200 })
+        })
+
+        it("should extract exported const enum", () => {
+            const code = `export const enum LogLevel {
+                Debug = 0,
+                Info = 1,
+                Warn = 2,
+                Error = 3
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].isExported).toBe(true)
+            expect(ast.enums[0].isConst).toBe(true)
+        })
+
+        it("should extract line range for enum", () => {
+            const code = `enum Test {
+                A = 1,
+                B = 2
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums[0].lineStart).toBe(1)
+            expect(ast.enums[0].lineEnd).toBe(4)
+        })
+
+        it("should handle enum with negative values", () => {
+            const code = `enum Temperature {
+                Cold = -10,
+                Freezing = -20,
+                Hot = 40
+            }`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].members[0]).toMatchObject({ name: "Cold", value: -10 })
+            expect(ast.enums[0].members[1]).toMatchObject({ name: "Freezing", value: -20 })
+            expect(ast.enums[0].members[2]).toMatchObject({ name: "Hot", value: 40 })
+        })
+
+        it("should handle empty enum", () => {
+            const code = `enum Empty {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.enums).toHaveLength(1)
+            expect(ast.enums[0].name).toBe("Empty")
+            expect(ast.enums[0].members).toHaveLength(0)
+        })
+
+        it("should not extract enum from JavaScript", () => {
+            const code = `enum Status { Active = 1 }`
+            const ast = parser.parse(code, "js")
+
+            expect(ast.enums).toHaveLength(0)
+        })
+    })
+
+    describe("decorators (0.24.4)", () => {
+        it("should extract class decorator", () => {
+            const code = `@Controller('users')
+class UserController {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].decorators).toHaveLength(1)
+            expect(ast.classes[0].decorators[0]).toBe("@Controller('users')")
+        })
+
+        it("should extract multiple class decorators", () => {
+            const code = `@Controller('api')
+@Injectable()
+@UseGuards(AuthGuard)
+class ApiController {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].decorators).toHaveLength(3)
+            expect(ast.classes[0].decorators[0]).toBe("@Controller('api')")
+            expect(ast.classes[0].decorators[1]).toBe("@Injectable()")
+            expect(ast.classes[0].decorators[2]).toBe("@UseGuards(AuthGuard)")
+        })
+
+        it("should extract method decorators", () => {
+            const code = `class UserController {
+    @Get(':id')
+    @Auth()
+    async getUser() {}
+}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].methods).toHaveLength(1)
+            expect(ast.classes[0].methods[0].decorators).toHaveLength(2)
+            expect(ast.classes[0].methods[0].decorators[0]).toBe("@Get(':id')")
+            expect(ast.classes[0].methods[0].decorators[1]).toBe("@Auth()")
+        })
+
+        it("should extract exported decorated class", () => {
+            const code = `@Injectable()
+export class UserService {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].isExported).toBe(true)
+            expect(ast.classes[0].decorators).toHaveLength(1)
+            expect(ast.classes[0].decorators[0]).toBe("@Injectable()")
+        })
+
+        it("should extract decorator with complex arguments", () => {
+            const code = `@Module({
+    imports: [UserModule],
+    controllers: [AppController],
+    providers: [AppService]
+})
+class AppModule {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].decorators).toHaveLength(1)
+            expect(ast.classes[0].decorators[0]).toContain("@Module")
+            expect(ast.classes[0].decorators[0]).toContain("imports")
+        })
+
+        it("should extract decorated class with extends", () => {
+            const code = `@Entity()
+class User extends BaseEntity {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].extends).toBe("BaseEntity")
+            expect(ast.classes[0].decorators).toHaveLength(1)
+            expect(ast.classes[0].decorators![0]).toBe("@Entity()")
+        })
+
+        it("should handle class without decorators", () => {
+            const code = `class SimpleClass {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].decorators).toHaveLength(0)
+        })
+
+        it("should handle method without decorators", () => {
+            const code = `class SimpleClass {
+    simpleMethod() {}
+}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].methods).toHaveLength(1)
+            expect(ast.classes[0].methods[0].decorators).toHaveLength(0)
+        })
+
+        it("should handle function without decorators", () => {
+            const code = `function simpleFunc() {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.functions).toHaveLength(1)
+            expect(ast.functions[0].decorators).toHaveLength(0)
+        })
+
+        it("should handle arrow function without decorators", () => {
+            const code = `const arrowFn = () => {}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.functions).toHaveLength(1)
+            expect(ast.functions[0].decorators).toHaveLength(0)
+        })
+
+        it("should extract NestJS controller pattern", () => {
+            const code = `@Controller('users')
+export class UserController {
+    @Get()
+    findAll() {}
+
+    @Get(':id')
+    findOne() {}
+
+    @Post()
+    @Body()
+    create() {}
+}`
+            const ast = parser.parse(code, "ts")
+
+            expect(ast.classes).toHaveLength(1)
+            expect(ast.classes[0].decorators).toContain("@Controller('users')")
+            expect(ast.classes[0].methods).toHaveLength(3)
+            expect(ast.classes[0].methods[0].decorators).toContain("@Get()")
+            expect(ast.classes[0].methods[1].decorators).toContain("@Get(':id')")
+            expect(ast.classes[0].methods[2].decorators).toContain("@Post()")
+        })
+    })
 })

packages/ipuaro/tests/unit/infrastructure/indexer/MetaAnalyzer.test.ts

@@ -3,6 +3,7 @@ import { MetaAnalyzer } from "../../../../src/infrastructure/indexer/MetaAnalyze
 import { ASTParser } from "../../../../src/infrastructure/indexer/ASTParser.js"
 import type { FileAST } from "../../../../src/domain/value-objects/FileAST.js"
 import { createEmptyFileAST } from "../../../../src/domain/value-objects/FileAST.js"
+import { createFileMeta, type FileMeta } from "../../../../src/domain/value-objects/FileMeta.js"
 
 describe("MetaAnalyzer", () => {
     let analyzer: MetaAnalyzer
@@ -737,4 +738,368 @@ export function createComponent(): MyComponent {
             expect(meta.fileType).toBe("source")
         })
     })
+
+    describe("computeTransitiveCounts", () => {
+        it("should compute transitive dependents for a simple chain", () => {
+            // A -> B -> C (A depends on B, B depends on C)
+            // So C has transitive dependents: B, A
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/b.ts"],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            expect(metas.get("/project/c.ts")!.transitiveDepCount).toBe(2) // B and A
+            expect(metas.get("/project/b.ts")!.transitiveDepCount).toBe(1) // A
+            expect(metas.get("/project/a.ts")!.transitiveDepCount).toBe(0) // none
+        })
+
+        it("should compute transitive dependencies for a simple chain", () => {
+            // A -> B -> C (A depends on B, B depends on C)
+            // So A has transitive dependencies: B, C
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/b.ts"],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(2) // B and C
+            expect(metas.get("/project/b.ts")!.transitiveDepByCount).toBe(1) // C
+            expect(metas.get("/project/c.ts")!.transitiveDepByCount).toBe(0) // none
+        })
+
+        it("should handle diamond dependency pattern", () => {
+            //     A
+            //    / \
+            //   B   C
+            //    \ /
+            //     D
+            // A depends on B and C, both depend on D
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts", "/project/c.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/d.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: ["/project/d.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/d.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/b.ts", "/project/c.ts"],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            // D is depended on by B, C, and transitively by A
+            expect(metas.get("/project/d.ts")!.transitiveDepCount).toBe(3)
+            // A depends on B, C, and transitively on D
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(3)
+        })
+
+        it("should handle circular dependencies gracefully", () => {
+            // A -> B -> C -> A (circular)
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts"],
+                    dependents: ["/project/c.ts"],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: ["/project/a.ts"],
+                    dependents: ["/project/b.ts"],
+                }),
+            )
+
+            // Should not throw, should handle cycles
+            analyzer.computeTransitiveCounts(metas)
+
+            // Each file has the other 2 as transitive dependents
+            expect(metas.get("/project/a.ts")!.transitiveDepCount).toBe(2)
+            expect(metas.get("/project/b.ts")!.transitiveDepCount).toBe(2)
+            expect(metas.get("/project/c.ts")!.transitiveDepCount).toBe(2)
+        })
+
+        it("should return 0 for files with no dependencies", () => {
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: [],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            expect(metas.get("/project/a.ts")!.transitiveDepCount).toBe(0)
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(0)
+        })
+
+        it("should handle empty metas map", () => {
+            const metas = new Map<string, FileMeta>()
+            // Should not throw
+            expect(() => analyzer.computeTransitiveCounts(metas)).not.toThrow()
+        })
+
+        it("should handle single file", () => {
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: [],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            expect(metas.get("/project/a.ts")!.transitiveDepCount).toBe(0)
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(0)
+        })
+
+        it("should handle multiple roots depending on same leaf", () => {
+            // A -> C, B -> C
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/a.ts", "/project/b.ts"],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            expect(metas.get("/project/c.ts")!.transitiveDepCount).toBe(2) // A and B
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(1) // C
+            expect(metas.get("/project/b.ts")!.transitiveDepByCount).toBe(1) // C
+        })
+
+        it("should handle deep dependency chains", () => {
+            // A -> B -> C -> D -> E
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/c.ts"],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+            metas.set(
+                "/project/c.ts",
+                createFileMeta({
+                    dependencies: ["/project/d.ts"],
+                    dependents: ["/project/b.ts"],
+                }),
+            )
+            metas.set(
+                "/project/d.ts",
+                createFileMeta({
+                    dependencies: ["/project/e.ts"],
+                    dependents: ["/project/c.ts"],
+                }),
+            )
+            metas.set(
+                "/project/e.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/d.ts"],
+                }),
+            )
+
+            analyzer.computeTransitiveCounts(metas)
+
+            // E has transitive dependents: D, C, B, A
+            expect(metas.get("/project/e.ts")!.transitiveDepCount).toBe(4)
+            // A has transitive dependencies: B, C, D, E
+            expect(metas.get("/project/a.ts")!.transitiveDepByCount).toBe(4)
+        })
+    })
+
+    describe("getTransitiveDependents", () => {
+        it("should return empty set for file not in metas", () => {
+            const metas = new Map<string, FileMeta>()
+            const cache = new Map<string, Set<string>>()
+
+            const result = analyzer.getTransitiveDependents("/project/unknown.ts", metas, cache)
+
+            expect(result.size).toBe(0)
+        })
+
+        it("should use cache for repeated calls", () => {
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/b.ts"],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: ["/project/a.ts"],
+                    dependents: [],
+                }),
+            )
+
+            const cache = new Map<string, Set<string>>()
+            const result1 = analyzer.getTransitiveDependents("/project/a.ts", metas, cache)
+            const result2 = analyzer.getTransitiveDependents("/project/a.ts", metas, cache)
+
+            // Should return same instance from cache
+            expect(result1).toBe(result2)
+            expect(result1.size).toBe(1)
+        })
+    })
+
+    describe("getTransitiveDependencies", () => {
+        it("should return empty set for file not in metas", () => {
+            const metas = new Map<string, FileMeta>()
+            const cache = new Map<string, Set<string>>()
+
+            const result = analyzer.getTransitiveDependencies("/project/unknown.ts", metas, cache)
+
+            expect(result.size).toBe(0)
+        })
+
+        it("should use cache for repeated calls", () => {
+            const metas = new Map<string, FileMeta>()
+            metas.set(
+                "/project/a.ts",
+                createFileMeta({
+                    dependencies: ["/project/b.ts"],
+                    dependents: [],
+                }),
+            )
+            metas.set(
+                "/project/b.ts",
+                createFileMeta({
+                    dependencies: [],
+                    dependents: ["/project/a.ts"],
+                }),
+            )
+
+            const cache = new Map<string, Set<string>>()
+            const result1 = analyzer.getTransitiveDependencies("/project/a.ts", metas, cache)
+            const result2 = analyzer.getTransitiveDependencies("/project/a.ts", metas, cache)
+
+            // Should return same instance from cache
+            expect(result1).toBe(result2)
+            expect(result1.size).toBe(1)
+        })
+    })
+
+    describe("analyzeAll with transitive counts", () => {
+        it("should compute transitive counts in analyzeAll", () => {
+            const files = new Map<string, { ast: FileAST; content: string }>()
+
+            // A imports B, B imports C
+            const aContent = `import { b } from "./b"`
+            const aAST = parser.parse(aContent, "ts")
+            files.set("/project/src/a.ts", { ast: aAST, content: aContent })
+
+            const bContent = `import { c } from "./c"\nexport const b = () => c()`
+            const bAST = parser.parse(bContent, "ts")
+            files.set("/project/src/b.ts", { ast: bAST, content: bContent })
+
+            const cContent = `export const c = () => 42`
+            const cAST = parser.parse(cContent, "ts")
+            files.set("/project/src/c.ts", { ast: cAST, content: cContent })
+
+            const results = analyzer.analyzeAll(files)
+
+            // C has transitive dependents: B and A
+            expect(results.get("/project/src/c.ts")!.transitiveDepCount).toBe(2)
+            // A has transitive dependencies: B and C
+            expect(results.get("/project/src/a.ts")!.transitiveDepByCount).toBe(2)
+        })
+    })
 })

packages/ipuaro/tests/unit/infrastructure/indexer/Watchdog.test.ts

@@ -109,24 +109,80 @@ describe("Watchdog", () => {
 
     describe("flushAll", () => {
         it("should not throw when no pending changes", () => {
+            watchdog.start(tempDir)
             expect(() => watchdog.flushAll()).not.toThrow()
         })
 
-        it("should flush all pending changes", async () => {
+        it("should handle flushAll with active timers", async () => {
+            const slowWatchdog = new Watchdog({ debounceMs: 1000 })
             const events: FileChangeEvent[] = []
-            watchdog.onFileChange((event) => events.push(event))
-            watchdog.start(tempDir)
+            slowWatchdog.onFileChange((event) => events.push(event))
+            slowWatchdog.start(tempDir)
+
+            await new Promise((resolve) => setTimeout(resolve, 200))
+
+            const testFile = path.join(tempDir, "instant-flush.ts")
+            await fs.writeFile(testFile, "const x = 1")
+
+            await new Promise((resolve) => setTimeout(resolve, 150))
+
+            const pendingCount = slowWatchdog.getPendingCount()
+            if (pendingCount > 0) {
+                slowWatchdog.flushAll()
+                expect(slowWatchdog.getPendingCount()).toBe(0)
+                expect(events.length).toBeGreaterThan(0)
+            }
+
+            await slowWatchdog.stop()
+        })
+
+        it("should flush all pending changes immediately", async () => {
+            const slowWatchdog = new Watchdog({ debounceMs: 500 })
+            const events: FileChangeEvent[] = []
+            slowWatchdog.onFileChange((event) => events.push(event))
+            slowWatchdog.start(tempDir)
 
             await new Promise((resolve) => setTimeout(resolve, 100))
 
-            const testFile = path.join(tempDir, "flush-test.ts")
+            const testFile1 = path.join(tempDir, "flush-test1.ts")
+            const testFile2 = path.join(tempDir, "flush-test2.ts")
+            await fs.writeFile(testFile1, "const x = 1")
+            await fs.writeFile(testFile2, "const y = 2")
+
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            const pendingCount = slowWatchdog.getPendingCount()
+            if (pendingCount > 0) {
+                slowWatchdog.flushAll()
+                expect(slowWatchdog.getPendingCount()).toBe(0)
+            }
+
+            await slowWatchdog.stop()
+        })
+
+        it("should clear all timers when flushing", async () => {
+            const slowWatchdog = new Watchdog({ debounceMs: 500 })
+            const events: FileChangeEvent[] = []
+            slowWatchdog.onFileChange((event) => events.push(event))
+            slowWatchdog.start(tempDir)
+
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            const testFile = path.join(tempDir, "timer-test.ts")
             await fs.writeFile(testFile, "const x = 1")
 
-            await new Promise((resolve) => setTimeout(resolve, 20))
+            await new Promise((resolve) => setTimeout(resolve, 100))
 
-            watchdog.flushAll()
+            const pendingBefore = slowWatchdog.getPendingCount()
 
-            await new Promise((resolve) => setTimeout(resolve, 50))
+            if (pendingBefore > 0) {
+                const eventsBefore = events.length
+                slowWatchdog.flushAll()
+                expect(slowWatchdog.getPendingCount()).toBe(0)
+                expect(events.length).toBeGreaterThan(eventsBefore)
+            }
+
+            await slowWatchdog.stop()
         })
     })
 
@@ -145,7 +201,7 @@ describe("Watchdog", () => {
             await customWatchdog.stop()
         })
 
-        it("should handle simple directory patterns", async () => {
+        it("should handle simple directory patterns without wildcards", async () => {
             const customWatchdog = new Watchdog({
                 debounceMs: 50,
                 ignorePatterns: ["node_modules", "dist"],
@@ -158,6 +214,48 @@ describe("Watchdog", () => {
 
             await customWatchdog.stop()
         })
+
+        it("should handle mixed wildcard and non-wildcard patterns", async () => {
+            const customWatchdog = new Watchdog({
+                debounceMs: 50,
+                ignorePatterns: ["node_modules", "*.log", "**/*.tmp", "dist", "build"],
+            })
+
+            customWatchdog.start(tempDir)
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            expect(customWatchdog.isWatching()).toBe(true)
+
+            await customWatchdog.stop()
+        })
+
+        it("should handle patterns with dots correctly", async () => {
+            const customWatchdog = new Watchdog({
+                debounceMs: 50,
+                ignorePatterns: ["*.test.ts", "**/*.spec.js"],
+            })
+
+            customWatchdog.start(tempDir)
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            expect(customWatchdog.isWatching()).toBe(true)
+
+            await customWatchdog.stop()
+        })
+
+        it("should handle double wildcards correctly", async () => {
+            const customWatchdog = new Watchdog({
+                debounceMs: 50,
+                ignorePatterns: ["**/node_modules/**", "**/.git/**"],
+            })
+
+            customWatchdog.start(tempDir)
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            expect(customWatchdog.isWatching()).toBe(true)
+
+            await customWatchdog.stop()
+        })
     })
 
     describe("file change detection", () => {
@@ -333,4 +431,94 @@ describe("Watchdog", () => {
             }
         })
     })
+
+    describe("error handling", () => {
+        it("should handle watcher errors gracefully", async () => {
+            const consoleErrorSpy = vi.spyOn(console, "error").mockImplementation(() => {})
+
+            watchdog.start(tempDir)
+
+            const watcher = (watchdog as any).watcher
+            if (watcher) {
+                watcher.emit("error", new Error("Test watcher error"))
+            }
+
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            expect(consoleErrorSpy).toHaveBeenCalledWith(
+                expect.stringContaining("Test watcher error"),
+            )
+
+            consoleErrorSpy.mockRestore()
+        })
+    })
+
+    describe("polling mode", () => {
+        it("should support polling mode", () => {
+            const pollingWatchdog = new Watchdog({
+                debounceMs: 50,
+                usePolling: true,
+                pollInterval: 500,
+            })
+
+            pollingWatchdog.start(tempDir)
+            expect(pollingWatchdog.isWatching()).toBe(true)
+
+            pollingWatchdog.stop()
+        })
+    })
+
+    describe("edge cases", () => {
+        it("should handle flushing non-existent change", () => {
+            watchdog.start(tempDir)
+            const flushChange = (watchdog as any).flushChange.bind(watchdog)
+            expect(() => flushChange("/non/existent/path.ts")).not.toThrow()
+        })
+
+        it("should handle clearing timer for same file multiple times", async () => {
+            const events: FileChangeEvent[] = []
+            watchdog.onFileChange((event) => events.push(event))
+            watchdog.start(tempDir)
+
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            const testFile = path.join(tempDir, "test.ts")
+            await fs.writeFile(testFile, "const x = 1")
+            await new Promise((resolve) => setTimeout(resolve, 10))
+            await fs.writeFile(testFile, "const x = 2")
+            await new Promise((resolve) => setTimeout(resolve, 10))
+            await fs.writeFile(testFile, "const x = 3")
+
+            await new Promise((resolve) => setTimeout(resolve, 200))
+
+            expect(events.length).toBeGreaterThanOrEqual(0)
+        })
+
+        it("should normalize file paths", async () => {
+            const events: FileChangeEvent[] = []
+            watchdog.onFileChange((event) => {
+                events.push(event)
+                expect(path.isAbsolute(event.path)).toBe(true)
+            })
+            watchdog.start(tempDir)
+
+            await new Promise((resolve) => setTimeout(resolve, 100))
+
+            const testFile = path.join(tempDir, "normalize-test.ts")
+            await fs.writeFile(testFile, "const x = 1")
+
+            await new Promise((resolve) => setTimeout(resolve, 200))
+        })
+
+        it("should handle empty directory", async () => {
+            const emptyDir = await fs.mkdtemp(path.join(os.tmpdir(), "empty-"))
+            const emptyWatchdog = new Watchdog({ debounceMs: 50 })
+
+            emptyWatchdog.start(emptyDir)
+            expect(emptyWatchdog.isWatching()).toBe(true)
+
+            await emptyWatchdog.stop()
+            await fs.rm(emptyDir, { recursive: true, force: true })
+        })
+    })
 })

packages/ipuaro/tests/unit/infrastructure/llm/OllamaClient.test.ts

@@ -95,53 +95,36 @@ describe("OllamaClient", () => {
             )
         })
 
-        it("should pass tools when provided", async () => {
+        it("should not pass tools parameter (tools are in system prompt)", async () => {
             const client = new OllamaClient(defaultConfig)
             const messages = [createUserMessage("Read file")]
-            const tools = [
-                {
-                    name: "get_lines",
-                    description: "Get lines from file",
-                    parameters: [
-                        {
-                            name: "path",
-                            type: "string" as const,
-                            description: "File path",
-                            required: true,
-                        },
-                    ],
-                },
-            ]
 
-            await client.chat(messages, tools)
+            await client.chat(messages)
 
             expect(mockOllamaInstance.chat).toHaveBeenCalledWith(
                 expect.objectContaining({
-                    tools: expect.arrayContaining([
+                    model: "qwen2.5-coder:7b-instruct",
+                    messages: expect.arrayContaining([
                         expect.objectContaining({
-                            type: "function",
-                            function: expect.objectContaining({
-                                name: "get_lines",
-                            }),
+                            role: "user",
+                            content: "Read file",
                         }),
                     ]),
                 }),
             )
+            expect(mockOllamaInstance.chat).toHaveBeenCalledWith(
+                expect.not.objectContaining({
+                    tools: expect.anything(),
+                }),
+            )
         })
 
-        it("should extract tool calls from response", async () => {
+        it("should extract tool calls from XML in response content", async () => {
             mockOllamaInstance.chat.mockResolvedValue({
                 message: {
                     role: "assistant",
-                    content: "",
-                    tool_calls: [
-                        {
-                            function: {
-                                name: "get_lines",
-                                arguments: { path: "src/index.ts" },
-                            },
-                        },
-                    ],
+                    content: '<tool_call name="get_lines"><path>src/index.ts</path></tool_call>',
+                    tool_calls: undefined,
                 },
                 eval_count: 30,
             })
@@ -424,48 +407,6 @@ describe("OllamaClient", () => {
         })
     })
 
-    describe("tool parameter conversion", () => {
-        it("should include enum values when present", async () => {
-            const client = new OllamaClient(defaultConfig)
-            const messages = [createUserMessage("Get status")]
-            const tools = [
-                {
-                    name: "get_status",
-                    description: "Get status",
-                    parameters: [
-                        {
-                            name: "type",
-                            type: "string" as const,
-                            description: "Status type",
-                            required: true,
-                            enum: ["active", "inactive", "pending"],
-                        },
-                    ],
-                },
-            ]
-
-            await client.chat(messages, tools)
-
-            expect(mockOllamaInstance.chat).toHaveBeenCalledWith(
-                expect.objectContaining({
-                    tools: expect.arrayContaining([
-                        expect.objectContaining({
-                            function: expect.objectContaining({
-                                parameters: expect.objectContaining({
-                                    properties: expect.objectContaining({
-                                        type: expect.objectContaining({
-                                            enum: ["active", "inactive", "pending"],
-                                        }),
-                                    }),
-                                }),
-                            }),
-                        }),
-                    ]),
-                }),
-            )
-        })
-    })
-
     describe("error handling", () => {
         it("should handle ECONNREFUSED errors", async () => {
             mockOllamaInstance.chat.mockRejectedValue(new Error("ECONNREFUSED"))
@@ -484,5 +425,27 @@ describe("OllamaClient", () => {
 
             await expect(client.pullModel("test")).rejects.toThrow(/Failed to pull model/)
         })
+
+        it("should handle AbortError correctly", async () => {
+            const abortError = new Error("aborted")
+            abortError.name = "AbortError"
+            mockOllamaInstance.chat.mockRejectedValue(abortError)
+
+            const client = new OllamaClient(defaultConfig)
+
+            await expect(client.chat([createUserMessage("Hello")])).rejects.toThrow(
+                /Request was aborted/,
+            )
+        })
+
+        it("should handle model not found errors", async () => {
+            mockOllamaInstance.chat.mockRejectedValue(new Error("model 'unknown' not found"))
+
+            const client = new OllamaClient(defaultConfig)
+
+            await expect(client.chat([createUserMessage("Hello")])).rejects.toThrow(
+                /Model.*not found/,
+            )
+        })
     })
 })

packages/ipuaro/tests/unit/infrastructure/llm/ResponseParser.test.ts

@@ -72,7 +72,7 @@ describe("ResponseParser", () => {
         })
 
         it("should parse null values", () => {
-            const response = `<tool_call name="test">
+            const response = `<tool_call name="get_lines">
                 <value>null</value>
             </tool_call>`
 
@@ -92,7 +92,7 @@ describe("ResponseParser", () => {
         })
 
         it("should parse JSON objects", () => {
-            const response = `<tool_call name="test">
+            const response = `<tool_call name="get_lines">
                 <config>{"key": "value"}</config>
             </tool_call>`
 
@@ -123,6 +123,161 @@ describe("ResponseParser", () => {
                 start: 5,
             })
         })
+
+        it("should reject unknown tool names", () => {
+            const response = `<tool_call name="unknown_tool"><path>test.ts</path></tool_call>`
+
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(0)
+            expect(result.hasParseErrors).toBe(true)
+            expect(result.parseErrors[0]).toContain("Unknown tool")
+            expect(result.parseErrors[0]).toContain("unknown_tool")
+        })
+
+        it("should normalize tool name aliases", () => {
+            // get_functions -> get_lines (common LLM typo)
+            const response1 = `<tool_call name="get_functions"><path>src/index.ts</path></tool_call>`
+            const result1 = parseToolCalls(response1)
+            expect(result1.toolCalls).toHaveLength(1)
+            expect(result1.toolCalls[0].name).toBe("get_lines")
+            expect(result1.hasParseErrors).toBe(false)
+
+            // read_file -> get_lines
+            const response2 = `<tool_call name="read_file"><path>test.ts</path></tool_call>`
+            const result2 = parseToolCalls(response2)
+            expect(result2.toolCalls).toHaveLength(1)
+            expect(result2.toolCalls[0].name).toBe("get_lines")
+
+            // find_todos -> get_todos
+            const response3 = `<tool_call name="find_todos"></tool_call>`
+            const result3 = parseToolCalls(response3)
+            expect(result3.toolCalls).toHaveLength(1)
+            expect(result3.toolCalls[0].name).toBe("get_todos")
+
+            // list_files -> get_structure
+            const response4 = `<tool_call name="list_files"><path>.</path></tool_call>`
+            const result4 = parseToolCalls(response4)
+            expect(result4.toolCalls).toHaveLength(1)
+            expect(result4.toolCalls[0].name).toBe("get_structure")
+        })
+
+        // JSON format tests
+        it("should parse JSON format tool calls as fallback", () => {
+            const response = `{"name": "get_lines", "arguments": {"path": "src/index.ts"}}`
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+            expect(result.toolCalls[0].params).toEqual({ path: "src/index.ts" })
+            expect(result.hasParseErrors).toBe(false)
+        })
+
+        it("should parse JSON format with numeric arguments", () => {
+            const response = `{"name": "get_lines", "arguments": {"path": "src/index.ts", "start": 1, "end": 50}}`
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].params).toEqual({
+                path: "src/index.ts",
+                start: 1,
+                end: 50,
+            })
+        })
+
+        it("should parse JSON format with surrounding text", () => {
+            const response = `I'll read the file for you:
+{"name": "get_lines", "arguments": {"path": "src/index.ts"}}
+Let me know if you need more.`
+
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+            expect(result.content).toContain("I'll read the file for you:")
+            expect(result.content).toContain("Let me know if you need more.")
+        })
+
+        it("should normalize tool name aliases in JSON format", () => {
+            // read_file -> get_lines
+            const response = `{"name": "read_file", "arguments": {"path": "test.ts"}}`
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+        })
+
+        it("should reject unknown tool names in JSON format", () => {
+            const response = `{"name": "unknown_tool", "arguments": {"path": "test.ts"}}`
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(0)
+            expect(result.hasParseErrors).toBe(true)
+            expect(result.parseErrors[0]).toContain("unknown_tool")
+        })
+
+        it("should prefer XML over JSON when both present", () => {
+            const response = `<tool_call name="get_lines"><path>xml.ts</path></tool_call>
+{"name": "get_function", "arguments": {"path": "json.ts", "name": "foo"}}`
+
+            const result = parseToolCalls(response)
+
+            // Should only parse XML since it was found first
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+            expect(result.toolCalls[0].params.path).toBe("xml.ts")
+        })
+
+        it("should parse JSON with empty arguments", () => {
+            const response = `{"name": "git_status", "arguments": {}}`
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("git_status")
+            expect(result.toolCalls[0].params).toEqual({})
+        })
+
+        it("should support CDATA for multiline content", () => {
+            const response = `<tool_call name="edit_lines">
+                <path>src/index.ts</path>
+                <content><![CDATA[const x = 1;
+const y = 2;]]></content>
+            </tool_call>`
+
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls[0].params.content).toBe("const x = 1;\nconst y = 2;")
+        })
+
+        it("should handle multiple tool calls with mixed content", () => {
+            const response = `Some text
+<tool_call name="get_lines"><path>a.ts</path></tool_call>
+More text
+<tool_call name="get_function"><path>b.ts</path><name>foo</name></tool_call>`
+
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(2)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+            expect(result.toolCalls[1].name).toBe("get_function")
+            expect(result.content).toContain("Some text")
+            expect(result.content).toContain("More text")
+        })
+
+        it("should handle parse errors gracefully and continue", () => {
+            const response = `<tool_call name="unknown_tool1"><path>test.ts</path></tool_call>
+<tool_call name="get_lines"><path>valid.ts</path></tool_call>
+<tool_call name="unknown_tool2"><path>test2.ts</path></tool_call>`
+
+            const result = parseToolCalls(response)
+
+            expect(result.toolCalls).toHaveLength(1)
+            expect(result.toolCalls[0].name).toBe("get_lines")
+            expect(result.hasParseErrors).toBe(true)
+            expect(result.parseErrors).toHaveLength(2)
+            expect(result.parseErrors[0]).toContain("unknown_tool1")
+            expect(result.parseErrors[1]).toContain("unknown_tool2")
+        })
     })
 
     describe("formatToolCallsAsXml", () => {

packages/ipuaro/tests/unit/infrastructure/security/PathValidator.test.ts

@@ -0,0 +1,320 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest"
+import * as path from "node:path"
+import * as fs from "node:fs/promises"
+import * as os from "node:os"
+import {
+    PathValidator,
+    createPathValidator,
+    validatePath,
+} from "../../../../src/infrastructure/security/PathValidator.js"
+
+describe("PathValidator", () => {
+    let validator: PathValidator
+    let tempDir: string
+    let projectRoot: string
+
+    beforeEach(async () => {
+        tempDir = await fs.mkdtemp(path.join(os.tmpdir(), "pathvalidator-test-"))
+        projectRoot = path.join(tempDir, "project")
+        await fs.mkdir(projectRoot)
+        validator = new PathValidator(projectRoot)
+    })
+
+    afterEach(async () => {
+        await fs.rm(tempDir, { recursive: true, force: true })
+    })
+
+    describe("constructor", () => {
+        it("should resolve project root to absolute path", () => {
+            const relativeValidator = new PathValidator("./project")
+            expect(relativeValidator.getProjectRoot()).toBe(path.resolve("./project"))
+        })
+
+        it("should store project root", () => {
+            expect(validator.getProjectRoot()).toBe(projectRoot)
+        })
+    })
+
+    describe("validateSync", () => {
+        it("should validate relative path within project", () => {
+            const result = validator.validateSync("src/file.ts")
+            expect(result.status).toBe("valid")
+            expect(result.absolutePath).toBe(path.join(projectRoot, "src/file.ts"))
+            expect(result.relativePath).toBe(path.join("src", "file.ts"))
+        })
+
+        it("should validate nested relative paths", () => {
+            const result = validator.validateSync("src/components/Button.tsx")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should validate root level files", () => {
+            const result = validator.validateSync("package.json")
+            expect(result.status).toBe("valid")
+            expect(result.relativePath).toBe("package.json")
+        })
+
+        it("should reject empty path", () => {
+            const result = validator.validateSync("")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path is empty")
+        })
+
+        it("should reject whitespace-only path", () => {
+            const result = validator.validateSync("   ")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path is empty")
+        })
+
+        it("should reject path with .. traversal", () => {
+            const result = validator.validateSync("../outside")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path contains traversal patterns")
+        })
+
+        it("should reject path with embedded .. traversal", () => {
+            const result = validator.validateSync("src/../../../etc/passwd")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path contains traversal patterns")
+        })
+
+        it("should reject path starting with tilde", () => {
+            const result = validator.validateSync("~/secret/file")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path contains traversal patterns")
+        })
+
+        it("should reject absolute path outside project", () => {
+            const result = validator.validateSync("/etc/passwd")
+            expect(result.status).toBe("outside_project")
+            expect(result.reason).toBe("Path is outside project root")
+        })
+
+        it("should accept absolute path inside project", () => {
+            const absoluteInside = path.join(projectRoot, "src/file.ts")
+            const result = validator.validateSync(absoluteInside)
+            expect(result.status).toBe("valid")
+        })
+
+        it("should trim whitespace from path", () => {
+            const result = validator.validateSync("  src/file.ts  ")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle Windows-style backslashes", () => {
+            const result = validator.validateSync("src\\components\\file.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should reject path that resolves outside via symlink-like patterns", () => {
+            const result = validator.validateSync("src/./../../etc")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path contains traversal patterns")
+        })
+    })
+
+    describe("validate (async)", () => {
+        beforeEach(async () => {
+            await fs.mkdir(path.join(projectRoot, "src"), { recursive: true })
+            await fs.writeFile(path.join(projectRoot, "src/file.ts"), "// content")
+            await fs.mkdir(path.join(projectRoot, "dist"), { recursive: true })
+        })
+
+        it("should validate existing file", async () => {
+            const result = await validator.validate("src/file.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should reject non-existent file by default", async () => {
+            const result = await validator.validate("src/nonexistent.ts")
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path does not exist")
+        })
+
+        it("should allow non-existent file with allowNonExistent option", async () => {
+            const result = await validator.validate("src/newfile.ts", { allowNonExistent: true })
+            expect(result.status).toBe("valid")
+        })
+
+        it("should validate directory when requireDirectory is true", async () => {
+            const result = await validator.validate("src", { requireDirectory: true })
+            expect(result.status).toBe("valid")
+        })
+
+        it("should reject file when requireDirectory is true", async () => {
+            const result = await validator.validate("src/file.ts", { requireDirectory: true })
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path is not a directory")
+        })
+
+        it("should validate file when requireFile is true", async () => {
+            const result = await validator.validate("src/file.ts", { requireFile: true })
+            expect(result.status).toBe("valid")
+        })
+
+        it("should reject directory when requireFile is true", async () => {
+            const result = await validator.validate("src", { requireFile: true })
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path is not a file")
+        })
+
+        it("should handle permission errors gracefully", async () => {
+            const result = await validator.validate("src/../../../root/secret")
+            expect(result.status).toBe("invalid")
+        })
+
+        it("should still check traversal before existence", async () => {
+            const result = await validator.validate("../outside", { allowNonExistent: true })
+            expect(result.status).toBe("invalid")
+            expect(result.reason).toBe("Path contains traversal patterns")
+        })
+    })
+
+    describe("isWithin", () => {
+        it("should return true for path within project", () => {
+            expect(validator.isWithin("src/file.ts")).toBe(true)
+        })
+
+        it("should return true for project root itself", () => {
+            expect(validator.isWithin(".")).toBe(true)
+            expect(validator.isWithin("")).toBe(false)
+        })
+
+        it("should return false for path outside project", () => {
+            expect(validator.isWithin("/etc/passwd")).toBe(false)
+        })
+
+        it("should return false for traversal path", () => {
+            expect(validator.isWithin("../outside")).toBe(false)
+        })
+
+        it("should return false for empty path", () => {
+            expect(validator.isWithin("")).toBe(false)
+        })
+
+        it("should return false for tilde path", () => {
+            expect(validator.isWithin("~/file")).toBe(false)
+        })
+    })
+
+    describe("resolve", () => {
+        it("should resolve valid relative path to absolute", () => {
+            const result = validator.resolve("src/file.ts")
+            expect(result).toBe(path.join(projectRoot, "src/file.ts"))
+        })
+
+        it("should return null for invalid path", () => {
+            expect(validator.resolve("../outside")).toBeNull()
+        })
+
+        it("should return null for empty path", () => {
+            expect(validator.resolve("")).toBeNull()
+        })
+
+        it("should return null for path outside project", () => {
+            expect(validator.resolve("/etc/passwd")).toBeNull()
+        })
+    })
+
+    describe("relativize", () => {
+        it("should return relative path for valid input", () => {
+            const result = validator.relativize("src/file.ts")
+            expect(result).toBe(path.join("src", "file.ts"))
+        })
+
+        it("should handle absolute path within project", () => {
+            const absolutePath = path.join(projectRoot, "src/file.ts")
+            const result = validator.relativize(absolutePath)
+            expect(result).toBe(path.join("src", "file.ts"))
+        })
+
+        it("should return null for path outside project", () => {
+            expect(validator.relativize("/etc/passwd")).toBeNull()
+        })
+
+        it("should return null for traversal path", () => {
+            expect(validator.relativize("../outside")).toBeNull()
+        })
+    })
+
+    describe("edge cases", () => {
+        it("should handle path with multiple slashes", () => {
+            const result = validator.validateSync("src///file.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle path with dots in filename", () => {
+            const result = validator.validateSync("src/file.test.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle hidden files", () => {
+            const result = validator.validateSync(".gitignore")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle hidden directories", () => {
+            const result = validator.validateSync(".github/workflows/ci.yml")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle single dot current directory", () => {
+            const result = validator.validateSync("./src/file.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle project root as path", () => {
+            const result = validator.validateSync(projectRoot)
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle unicode characters in path", () => {
+            const result = validator.validateSync("src/файл.ts")
+            expect(result.status).toBe("valid")
+        })
+
+        it("should handle spaces in path", () => {
+            const result = validator.validateSync("src/my file.ts")
+            expect(result.status).toBe("valid")
+        })
+    })
+})
+
+describe("createPathValidator", () => {
+    it("should create PathValidator instance", () => {
+        const validator = createPathValidator("/tmp/project")
+        expect(validator).toBeInstanceOf(PathValidator)
+        expect(validator.getProjectRoot()).toBe("/tmp/project")
+    })
+})
+
+describe("validatePath", () => {
+    let tempDir: string
+    let projectRoot: string
+
+    beforeEach(async () => {
+        tempDir = await fs.mkdtemp(path.join(os.tmpdir(), "validatepath-test-"))
+        projectRoot = path.join(tempDir, "project")
+        await fs.mkdir(projectRoot)
+    })
+
+    afterEach(async () => {
+        await fs.rm(tempDir, { recursive: true, force: true })
+    })
+
+    it("should return true for valid path", () => {
+        expect(validatePath("src/file.ts", projectRoot)).toBe(true)
+    })
+
+    it("should return false for traversal path", () => {
+        expect(validatePath("../outside", projectRoot)).toBe(false)
+    })
+
+    it("should return false for path outside project", () => {
+        expect(validatePath("/etc/passwd", projectRoot)).toBe(false)
+    })
+
+    it("should return false for empty path", () => {
+        expect(validatePath("", projectRoot)).toBe(false)
+    })
+})

packages/ipuaro/tests/unit/infrastructure/tools/edit/CreateFileTool.test.ts

@@ -224,7 +224,7 @@ describe("CreateFileTool", () => {
             const result = await tool.execute({ path: "../outside/file.ts", content: "test" }, ctx)
 
             expect(result.success).toBe(false)
-            expect(result.error).toBe("Path must be within project root")
+            expect(result.error).toBe("Path contains traversal patterns")
         })
 
         it("should return error if file already exists", async () => {

packages/ipuaro/tests/unit/infrastructure/tools/edit/DeleteFileTool.test.ts

@@ -189,7 +189,7 @@ describe("DeleteFileTool", () => {
             const result = await tool.execute({ path: "../outside/file.ts" }, ctx)
 
             expect(result.success).toBe(false)
-            expect(result.error).toBe("Path must be within project root")
+            expect(result.error).toBe("Path contains traversal patterns")
         })
 
         it("should return error if file does not exist", async () => {

packages/ipuaro/tests/unit/infrastructure/tools/edit/EditLinesTool.test.ts

@@ -296,7 +296,7 @@ describe("EditLinesTool", () => {
             )
 
             expect(result.success).toBe(false)
-            expect(result.error).toBe("Path must be within project root")
+            expect(result.error).toBe("Path contains traversal patterns")
         })
 
         it("should return error when start exceeds file length", async () => {

packages/ipuaro/tests/unit/infrastructure/tools/read/GetClassTool.test.ts

@@ -271,7 +271,7 @@ describe("GetClassTool", () => {
             const result = await tool.execute({ path: "../outside/file.ts", name: "MyClass" }, ctx)
 
             expect(result.success).toBe(false)
-            expect(result.error).toBe("Path must be within project root")
+            expect(result.error).toBe("Path contains traversal patterns")
         })
 
         it("should handle class with no extends", async () => {
@@ -344,5 +344,47 @@ describe("GetClassTool", () => {
 
             expect(result.callId).toMatch(/^get_class-\d+$/)
         })
+
+        it("should handle undefined extends in class", async () => {
+            const lines = ["class StandaloneClass { method() {} }"]
+            const cls = createMockClass({
+                name: "StandaloneClass",
+                lineStart: 1,
+                lineEnd: 1,
+                extends: undefined,
+                methods: [{ name: "method", lineStart: 1, lineEnd: 1 }],
+            })
+            const ast = createMockAST([cls])
+            const storage = createMockStorage({ lines }, ast)
+            const ctx = createMockContext(storage)
+
+            const result = await tool.execute({ path: "test.ts", name: "StandaloneClass" }, ctx)
+
+            expect(result.success).toBe(true)
+            const data = result.data as GetClassResult
+            expect(data.extends).toBeUndefined()
+            expect(data.methods.length).toBe(1)
+        })
+
+        it("should handle error when reading lines fails", async () => {
+            const ast = createMockAST([createMockClass({ name: "Test", lineStart: 1, lineEnd: 1 })])
+            const storage: IStorage = {
+                getFile: vi.fn().mockResolvedValue(null),
+                getAST: vi.fn().mockResolvedValue(ast),
+                setFile: vi.fn(),
+                deleteFile: vi.fn(),
+                getAllFiles: vi.fn(),
+                setAST: vi.fn(),
+                getSymbolIndex: vi.fn(),
+                setSymbolIndex: vi.fn(),
+                getDepsGraph: vi.fn(),
+                setDepsGraph: vi.fn(),
+            }
+            const ctx = createMockContext(storage)
+
+            const result = await tool.execute({ path: "test.ts", name: "Test" }, ctx)
+
+            expect(result.success).toBe(false)
+        })
     })
 })