feat: normalize database schema for document-chunk separation (Issue-2) ...

- Added 'documents' table for metadata.
- Refactored 'items' table for chunk storage.
- Updated MCP tools (add_item_text, search_text, etc.) to support the new schema.
- Updated technical documentation.

Docs: Separate technical specifications from project operational workflows

Docs/Chore: Establish bilingual (Japanese/English) issue policy and update dev guide

Docs: Modernize all specification documents to align with LSA-based architecture and new directory structure

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

Fix: untrack docs/issues from git and add to gitignore

Feat: implement two-way issue sync tool with GitBucket

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