v1.0 Production Hardening

Delivered: Fixed 7 critical/high bugs to make codetree production-ready for agents.

Key accomplishments:
- threading.Lock on all 23 GraphStore methods (concurrent MCP safety)
- Path traversal validation on all 15 file_path tools (security)
- Qualified file::name definition keys (no duplicates, no ghosts, no collisions)
- Plugin crash isolation (server continues on plugin errors)
- 58 new regression tests, 1116 total, 0 regressions

See .planning/MILESTONES.md for full details.