Replace SQLite with JSON file storage

- Remove database.py (SQLite) from tools/storage/ and dss-mvp1/
- Add json_store.py with full JSON-based storage layer
- Update 16 files to use new json_store imports
- Storage now mirrors DSS canonical structure:
  .dss/data/
  ├── _system/    (config, cache, activity)
  ├── projects/   (per-project: tokens, components, styles)
  └── teams/      (team definitions)
- Remove Docker files (not needed)
- Update DSS_CORE.json to v1.1.0

Philosophy: "Eat our own food" - storage structure matches DSS design

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

tools/auth/atlassian_auth.py

@@ -12,7 +12,7 @@ from datetime import datetime, timedelta
 from typing import Optional, Dict, Any
 from atlassian import Jira, Confluence
 
-from storage.database import get_connection
+from storage.json_store import read_json, write_json, SYSTEM_DIR
 
 
 class AtlassianAuth: