chore(docs): add documentation links and improve code formatting

[raychrisgdp]

Summary

Issues & Goals:

• Improve documentation discoverability by adding standardized "Docs Links" sections to all PR specification files
• Enhance code consistency by applying ruff formatter across backend codebase
• Strengthen pre-commit checks to prevent accidental commits to main branch
• Improve README structure and documentation navigation
• Add automated review workflow commands for Cursor IDE

Implementation Highlights:

• Documentation Links: Added standardized "Docs Links" sections to all 17 PR specification files in docs/02-implementation/pr-specs/ with references to relevant design documents, user guides, and implementation guides
• Code Formatting: Applied ruff formatter across backend codebase (backend/cli/, backend/config.py, backend/database.py, backend/models/) to enforce consistent line length and formatting standards
• Pre-commit Enhancements: Added no-commit-to-branch hook to prevent accidental commits to main branch and updated Makefile to include docs-check in precommit workflow
• README Improvements: Restructured README.md with clearer documentation navigation, improved "What You Can Do Right Now" section, and better organization of documentation links
• New Cursor Commands: Added .cursor/commands/review-implement.md and .cursor/commands/review-validate.md for automated review workflow support
• Review Command Updates: Updated .cursor/commands/review.md to reflect project-specific patterns (Python 3.11+, ruff formatting, TaskGenie conventions) and simplified structure
• Test Updates: Updated test files to match formatting changes while preserving test functionality

How to Test

Documentation Review & Validation:

Since this PR contains primarily documentation and code formatting changes, reviewers should focus on:

1. Documentation Links Validation:

   • Review "Docs Links" sections in PR spec files (docs/02-implementation/pr-specs/PR-*.md)
   • Verify that all referenced documentation files exist and links are accurate
   • Check that links point to relevant design documents, user guides, and implementation guides
   • Validate that cross-references between PR specs and design docs are consistent
   • Spot-check several PR spec files (e.g., PR-001-db-config.md, PR-005-rag-semantic-search.md) to verify "Docs Links" sections are complete

2. Code Formatting Verification:

   • Run make format to ensure all files are properly formatted
   • Verify that ruff formatter changes don't alter code functionality
   • Check that multi-line function signatures are appropriately formatted according to line length rules (120 chars)
   • Review a sample of formatted files (e.g., backend/cli/db.py, backend/config.py, backend/models/task.py) to ensure formatting is consistent and readable
   • Confirm that formatting is consistent across backend modules

3. Pre-commit Configuration:

   • Test pre-commit hooks: make hooks then attempt a commit to verify no-commit-to-branch hook works
   • Verify make precommit includes docs-check: make precommit should run both docs validation and pre-commit checks
   • Confirm that existing pre-commit hooks still function correctly
   • Test that attempting to commit to main branch is blocked by the hook

4. README Structure:

   • Review README.md structure and verify documentation links are accurate
   • Check that "Docs Map" section provides clear navigation to key documentation files
   • Verify that "What You Can Do Right Now" section accurately reflects current capabilities
   • Confirm that "Try It Now" section provides helpful quickstart commands

5. Cursor Commands:

   • Review new cursor command files (.cursor/commands/review-implement.md, .cursor/commands/review-validate.md)
   • Verify command structure follows existing patterns
   • Check that commands integrate properly with review workflow
   • Review updated .cursor/commands/review.md to ensure project-specific patterns are correctly reflected and structure is simplified

6. Test Execution:

   • Run make test to ensure formatting changes don't break existing tests
   • Verify that test logic remains unchanged (only formatting updates)
   • Confirm that all tests pass without modification to test functionality

Expected Behavior:

• All PR spec files should have "Docs Links" sections with accurate references
• Code formatting should be consistent across all backend modules (120-char line limit)
• Pre-commit hooks should prevent commits to main branch
• make precommit should run both docs-check and pre-commit validation
• README.md should provide clear navigation to documentation
• All tests should pass without modification to test logic
• Cursor commands should follow consistent patterns and integrate with review workflow

Related Issues

• None

Author Checklist

• Synced with latest main branch
• Self-reviewed
• All tests pass locally
• Documentation updated (if applicable)
• No breaking changes (or documented if intentional)

Additional Notes

Key Implementation Areas for Review

Documentation Improvements:

• docs/02-implementation/pr-specs/*.md: Added "Docs Links" sections to all 17 PR specification files - verify links are accurate and complete
• docs/INDEX.md: Updated documentation index - verify cross-references are correct
• README.md: Restructured with improved navigation - verify structure is helpful for new users

Code Formatting:

• backend/cli/db.py, backend/cli/main.py: Applied ruff formatter - verify formatting is consistent and readable (function signatures reformatted to fit 120-char limit)
• backend/config.py, backend/database.py: Formatting changes - verify no functional changes
• backend/models/*.py: Model formatting updates - verify relationships and field definitions are preserved

Pre-commit & Tooling:

• .pre-commit-config.yaml: Added no-commit-to-branch hook - verify hook prevents commits to main
• Makefile: Updated precommit target to include docs-check - verify workflow integration
• pyproject.toml: Minor updates - verify configuration is correct

New Cursor Commands:

• .cursor/commands/review-implement.md: New command for implementing review findings - verify structure and integration
• .cursor/commands/review-validate.md: New command for validating reviews - verify workflow integration
• .cursor/commands/review.md: Updated to reflect project-specific patterns - verify Python 3.11+ and TaskGenie conventions are correctly documented, structure simplified

Test Updates:

• tests/cli/test_db.py, tests/cli/test_main.py: Formatting updates - verify tests still pass
• tests/models/*.py: Test formatting changes - verify test logic unchanged
• tests/test_config.py, tests/test_database.py: Formatting updates - verify functionality preserved
• tests/test_migrations_env.py: Formatting updates - verify migration testing still works

Testing Notes

• Worktree state: Modified files exist (.cursor/commands/pr-desc.md, .cursor/commands/review-implement.md) and untracked files (PR_DESCRIPTION.md, review files) but don't affect this PR
• Formatting-only changes: Most backend code changes are formatting-related (ruff formatter) - no functional changes expected
• Documentation-only changes: PR spec files only have "Docs Links" sections added - no content changes
• Pre-commit validation: New hook should be tested manually to verify it prevents commits to main branch
• Test execution: All tests should pass without modification to test logic - formatting changes should be transparent to test execution
• Cursor commands: New commands are documentation-only - verify they follow existing patterns and integrate with review workflow