notes: Update TODO

Author: tony

notes/TODO.md

@@ -4,16 +4,16 @@
 
 ## 1. Configuration Format & Structure
 
-- [ ] **Phase 1: Schema Definition**
-  - [ ] Define complete Pydantic v2 models for configuration
-  - [ ] Implement comprehensive validation logic
+- [x] **Phase 1: Schema Definition**
+  - [x] Define complete Pydantic v2 models for configuration
+  - [x] Implement comprehensive validation logic
   - [ ] Generate schema documentation from models
 
-- [ ] **Phase 2: Configuration Handling**
-  - [ ] Implement configuration loading functions
-  - [ ] Add environment variable support for configuration
-  - [ ] Create include resolution logic
-  - [ ] Develop configuration merging functions
+- [x] **Phase 2: Configuration Handling**
+  - [x] Implement configuration loading functions
+  - [x] Add environment variable support for configuration
+  - [x] Create include resolution logic
+  - [x] Develop configuration merging functions
 
 - [ ] **Phase 3: Migration Tools**
   - [ ] Create tools to convert old format to new format
@@ -22,62 +22,62 @@
 
 - [ ] **Phase 4: Documentation & Examples**
   - [ ] Generate JSON schema documentation
-  - [ ] Create example configuration files
+  - [x] Create example configuration files
   - [ ] Update user documentation with new format
 
 ## 2. Validation System
 
-- [ ] **Single Validation System**
-  - [ ] Migrate all validation to Pydantic v2 models
-  - [ ] Eliminate parallel validator.py module
-  - [ ] Use Pydantic's built-in validation capabilities
+- [x] **Single Validation System**
+  - [x] Migrate all validation to Pydantic v2 models
+  - [x] Eliminate parallel validator.py module
+  - [x] Use Pydantic's built-in validation capabilities
 
-- [ ] **Unified Error Handling**
-  - [ ] Standardize on exception-based error handling
-  - [ ] Create unified error handling module
-  - [ ] Implement consistent error formatting
+- [x] **Unified Error Handling**
+  - [x] Standardize on exception-based error handling
+  - [x] Create unified error handling module
+  - [x] Implement consistent error formatting
 
-- [ ] **Type System Enhancement**
-  - [ ] Create clear type aliases
-  - [ ] Define VCS handler protocols
-  - [ ] Implement shared TypeAdapters for critical paths
+- [x] **Type System Enhancement**
+  - [x] Create clear type aliases
+  - [x] Define VCS handler protocols
+  - [x] Implement shared TypeAdapters for critical paths
 
-- [ ] **Streamlined Model Hierarchy**
-  - [ ] Flatten object models
-  - [ ] Use composition over inheritance
-  - [ ] Implement computed fields for derived data
+- [x] **Streamlined Model Hierarchy**
+  - [x] Flatten object models
+  - [x] Use composition over inheritance
+  - [x] Implement computed fields for derived data
 
-- [ ] **Validation Pipeline**
-  - [ ] Simplify validation process flow
-  - [ ] Create clear API for validation
-  - [ ] Implement path expansion and normalization
+- [x] **Validation Pipeline**
+  - [x] Simplify validation process flow
+  - [x] Create clear API for validation
+  - [x] Implement path expansion and normalization
 
 ## 3. Testing System
 
-- [ ] **Restructured Test Organization**
-  - [ ] Reorganize tests to mirror source code structure
-  - [ ] Create separate unit, integration, and functional test directories
-  - [ ] Break up large test files into smaller, focused tests
+- [x] **Restructured Test Organization**
+  - [x] Reorganize tests to mirror source code structure
+  - [x] Create separate unit, integration, and functional test directories
+  - [x] Break up large test files into smaller, focused tests
 
-- [ ] **Improved Test Fixtures**
-  - [ ] Centralize fixture definitions in conftest.py
-  - [ ] Create factory fixtures for common objects
-  - [ ] Implement temporary directory helpers
+- [x] **Improved Test Fixtures**
+  - [x] Centralize fixture definitions in conftest.py
+  - [x] Create factory fixtures for common objects
+  - [x] Implement temporary directory helpers
 
-- [ ] **Test Isolation**
-  - [ ] Ensure tests don't interfere with each other
-  - [ ] Create isolated fixtures for filesystem operations
-  - [ ] Implement mocks for external dependencies
+- [x] **Test Isolation**
+  - [x] Ensure tests don't interfere with each other
+  - [x] Create isolated fixtures for filesystem operations
+  - [x] Implement mocks for external dependencies
 
 - [ ] **Property-Based Testing**
   - [ ] Integrate Hypothesis for property-based testing
   - [ ] Create generators for config data
   - [ ] Test invariants for configuration handling
 
-- [ ] **Integrated Documentation and Testing**
-  - [ ] Add doctests for key functions
-  - [ ] Create example-based tests
-  - [ ] Ensure examples serve as both documentation and tests
+- [x] **Integrated Documentation and Testing**
+  - [x] Add doctests for key functions
+  - [x] Create example-based tests
+  - [x] Ensure examples serve as both documentation and tests
 
 - [ ] **Enhanced CLI Testing**
   - [ ] Implement comprehensive CLI command tests
@@ -86,35 +86,35 @@
 
 ## 4. Internal APIs
 
-- [ ] **Consistent Module Structure**
-  - [ ] Reorganize codebase according to proposed structure
-  - [ ] Separate public and private API components
-  - [ ] Create logical module organization
+- [x] **Consistent Module Structure**
+  - [x] Reorganize codebase according to proposed structure
+  - [x] Separate public and private API components
+  - [x] Create logical module organization
 
-- [ ] **Function Design Improvements**
-  - [ ] Standardize function signatures
-  - [ ] Implement clear parameter and return types
-  - [ ] Add comprehensive docstrings with type information
+- [x] **Function Design Improvements**
+  - [x] Standardize function signatures
+  - [x] Implement clear parameter and return types
+  - [x] Add comprehensive docstrings with type information
 
-- [ ] **Module Responsibility Separation**
-  - [ ] Apply single responsibility principle
-  - [ ] Extract pure functions from complex methods
-  - [ ] Create focused modules with clear responsibilities
+- [x] **Module Responsibility Separation**
+  - [x] Apply single responsibility principle
+  - [x] Extract pure functions from complex methods
+  - [x] Create focused modules with clear responsibilities
 
 - [ ] **Dependency Injection**
   - [ ] Reduce global state dependencies
   - [ ] Implement dependency injection patterns
   - [ ] Make code more testable through explicit dependencies
 
-- [ ] **Enhanced Type System**
-  - [ ] Add comprehensive type annotations
-  - [ ] Create clear type hierarchies
-  - [ ] Define interfaces and protocols
+- [x] **Enhanced Type System**
+  - [x] Add comprehensive type annotations
+  - [x] Create clear type hierarchies
+  - [x] Define interfaces and protocols
 
-- [ ] **Error Handling Strategy**
-  - [ ] Create exception hierarchy
-  - [ ] Implement consistent error reporting
-  - [ ] Add context to exceptions
+- [x] **Error Handling Strategy**
+  - [x] Create exception hierarchy
+  - [x] Implement consistent error reporting
+  - [x] Add context to exceptions
 
 - [ ] **Event-Based Architecture**
   - [ ] Implement event system for cross-component communication
@@ -123,25 +123,25 @@
 
 ## 5. External APIs
 
-- [ ] **Public API Definition**
-  - [ ] Create dedicated API module
-  - [ ] Define public interfaces
-  - [ ] Create exports in __init__.py
+- [x] **Public API Definition**
+  - [x] Create dedicated API module
+  - [x] Define public interfaces
+  - [x] Create exports in __init__.py
 
-- [ ] **Configuration API**
-  - [ ] Implement load_config function
+- [x] **Configuration API**
+  - [x] Implement load_config function
   - [ ] Create save_config function
-  - [ ] Add validation helpers
+  - [x] Add validation helpers
 
 - [ ] **Repository Operations API**
   - [ ] Implement sync_repositories function
   - [ ] Create detect_repositories function
   - [ ] Add lock_repositories functionality
 
-- [ ] **Versioning Strategy**
-  - [ ] Implement semantic versioning
+- [x] **Versioning Strategy**
+  - [x] Implement semantic versioning
   - [ ] Create deprecation policy
-  - [ ] Add version information to API
+  - [x] Add version information to API
 
 - [ ] **Comprehensive Documentation**
   - [ ] Document all public APIs
@@ -214,12 +214,21 @@
 
 ## Implementation Timeline
 
-| Proposal | Priority | Estimated Effort | Dependencies |
-|----------|----------|------------------|--------------|
-| Validation System | High | 3 weeks | None |
-| Configuration Format | High | 2 weeks | Validation System |
-| Internal APIs | High | 4 weeks | Validation System |
-| Testing System | Medium | 3 weeks | None |
-| CLI System | Medium | 3 weeks | Internal APIs |
-| External APIs | Medium | 2 weeks | Internal APIs |
-| CLI Tools | Low | 2 weeks | CLI System |
+| Proposal | Priority | Estimated Effort | Dependencies | Status |
+|----------|----------|------------------|--------------|--------|
+| Validation System | High | 3 weeks | None | ✅ Completed |
+| Configuration Format | High | 2 weeks | Validation System | ✅ Mostly Complete |
+| Internal APIs | High | 4 weeks | Validation System | ✅ Mostly Complete |
+| Testing System | Medium | 3 weeks | None | ✅ Mostly Complete |
+| CLI System | Medium | 3 weeks | Internal APIs | 🟠 Not Started |
+| External APIs | Medium | 2 weeks | Internal APIs | 🟠 Partially Complete |
+| CLI Tools | Low | 2 weeks | CLI System | 🟠 Not Started |
+
+## Recent Progress
+
+- Added type system improvements:
+  - Created `py.typed` marker file to ensure proper type checking
+  - Implemented `ConfigDict` TypedDict in a new types module
+  - Fixed mypy errors and improved type annotations
+- All tests are now passing with no linter or mypy errors
+- Improved configuration handling with robust include resolution and merging