Enhance documentation, update skills, and refactor codebase - #15

- Updated CHANGELOG.md to reflect the removal of the Universal RAG Gateway module, replaced by a lighter embedded knowledge base solution.
- Modified package.json and README.md to remove references to the Universal RAG Gateway.
- Deleted associated files and configurations related to the Universal RAG Gateway from the project.

- Modified README.md to reflect changes in data storage from SQLite to a single JSON cache file.
- Updated sync command in README for consistency with new storage method.
- Adjusted parser to skip hidden directories related to the JSON cache.
- Enhanced search functionality to include planId filtering in search queries.
- Refactored store to accommodate JSON cache for entity storage instead of SQLite.

- Revised the instructions in AGENT-BRIEF.md to specify a seven-segment structure for PLAN.md, including Goal, Constraints & assumptions, Approach, Key decisions & tradeoffs, Validation plan, Risks, and Out of scope.

- Deleted PLAN.md and PLAN-REVIEW-LOG.md as part of the project restructuring. These files contained the plan for login rate limiting with Redis and associated review logs, which are no longer needed.

- Revised README.md to clarify the local embedded knowledge base's zero external service dependency and updated the configuration section for embedding API usage.
- Enhanced the config.ts file to load embedding secrets from env/secrets.json, allowing for programmatic overrides and improved handling of embedding API keys and URLs.

- Introduced new commands `visualize` and `codegraph` in the CLI for generating interactive knowledge and code architecture graphs, respectively.
- Updated package.json to include corresponding scripts.
- Enhanced CLI help output to document the new commands and their usage with an optional `--output` flag for custom file paths.

- Remove codegraph.ts (989 lines) and refactor CLI/extractor/parser/types
- Add search tests for plan-reviews
- Update plan-grill skill docs (SKILL.md, AGENT-BRIEF.md, plan_grill.md)
- Update cross-model-review and ios-engineer reference docs
- Add ios-engineer evolution proposal for PG-005 architecture analysis mode

- Changed the user path for the claude CLI tool from '/Users/song/.local/bin/claude' to '/Users/you/.local/bin/claude' in the regression-login-rate-limit.md example.