Add guarded repository reanalysis automation

[htsugawa]

Summary

• add guarded Catalog analysis-unit reanalysis planning and bounded MCP handoffs
• add automatic 3,000-6,000 peak-count tuning with instrument-aware threshold steps
• add official/source/custom Console selection with build provenance
• add auditable tiered LBM/MSP annotation configuration and UI support
• update the Claude/Codex skill, documentation, and regression tests

Safety and provenance

• keep repository analysis units isolated
• enforce configured workspace and size boundaries before download
• preserve analysis purpose, Class review, artifact ownership, and Console provenance
• never package or redistribute private MSP libraries

Tests

• python -m unittest discover -s tests -q (139 passed)
• node --check static/app.js

Dependency

This is a stacked PR on top of #9, which itself follows #8.