feat: incremental analysis — watch mode, parse only changed files

[bntvllnt]

Summary

Add incremental parsing that only re-analyzes files changed since last index, plus a watch mode for real-time updates.

Motivation

• Full re-parse on every run is wasteful for large repos
• codebase-memory-mcp caches persistently and updates incrementally
• Augment Code does initial index in 27 min, then incremental <20s
• Watch mode enables real-time metrics during development
• Essential for scaling to large repos (1000+ files)

Approach

1. Diff-based parsing: Compare git HEAD with cached index HEAD
2. Selective re-parse: Only parse files in git diff --name-only
3. Graph patching: Remove old nodes/edges for changed files, add new ones
4. Metric recomputation: PageRank/betweenness need full recompute (global), but blast radius can be scoped
5. Watch mode: codebase-intelligence watch <path> — re-index on file save

Challenges

• PageRank and betweenness are global metrics — can't be updated incrementally
• Graph structure changes (new imports) affect transitive metrics
• Tradeoff: approximate incremental metrics vs exact full recompute

Acceptance Criteria

• --incremental flag skips unchanged files
• watch CLI command for real-time updates
• 10x faster re-analysis for small changes on large repos
• Correctness: incremental results match full recompute (within tolerance for global metrics)
• Tests comparing incremental vs full results

Priority

Long-term — Essential for large repo adoption but current caching handles most cases.