refactor: Split mcp.rs into functional modules and sub-tools

docs: remove Japanese duplicate journal (keep ASCII copy)

docs: add missing journals and update sync script ...

- Added journals 0011 and 0012.
- Updated sync_issues.mjs for robust issue tracking.
- (Deleted closed issue files per cleanup rule).

Docs/Chore: Implement manual issue closure reminder and update development guide rules

Feat: implement two-way issue sync tool with GitBucket

Refactor: reorganization of root and source directories and fix Error 1412