Continue comprehensive pyright type checking implementation - Phases 3-6

[rysweet]

Continue the comprehensive pyright type checking implementation from Phases 3-6 to achieve zero type errors.

Current Status:

• Phase 1 (Foundation) and Phase 2 (Core Graph System) completed in PR feat: Implement comprehensive pyright type checking foundation #226
• Current error count: 1,084 pyright errors
• Target: Zero pyright errors across entire codebase

Remaining Phases:

• Phase 3: LLM and Filesystem Modules type fixes
• Phase 4: Analysis and Processing Modules
• Phase 5: Project Structure and Utilities
• Phase 6: Test Suite and final error resolution

Success Criteria:

• Zero pyright errors across entire codebase
• Complete type annotation coverage for all modules
• All tests pass with type annotations
• CI/CD enforces strict type checking

This continues the work from Issue #225 to achieve 100% pyright compliance.

Note: This issue was created by an AI agent on behalf of the repository owner.