fix(incremental): use git --name-status -M to detect renames + prune old-path nodes (#366)

[tirth8205]

Summary

Addresses Bug 1 of 3 from #366: renamed/moved files left orphaned
old-path nodes (plus every edge that referenced them) in the knowledge
graph after an incremental /understand run.

• Switch the incremental change-detection command in
  skills/understand/SKILL.md from git diff <base>..HEAD --name-only
  to git diff <base>..HEAD --name-status -M. The plain --name-only
  form reports a rename as only the new path, so the prune step never
  saw the old path; with -M the rename appears as
  R<score>\told\tnew and we can route the two paths to different
  buckets.
• Add a small parser helper skills/understand/parse-git-changes.mjs
  that splits the --name-status lines into two disjoint sets:
  • changed-files.txt — paths to analyze: M, A, T, U,
    plus the new path of R<score> renames and C<score> copies.
  • prune-files.txt — paths to prune-only: D deletions plus
    the old path of R<score> renames. Copies do not prune the
    source because the original file still exists.
• Update the Phase 2 incremental prune step to prune the union of both
  sets — re-analyzed files still need their old nodes dropped, and
  prune-only files need removal without a replacement.
• Add tests/skill/understand/test_parse_git_changes.test.mjs with
  16 cases covering all status branches (M / A / D / R / C / T / U /
  unknown / empty) plus a CLI round-trip. Fixtures are raw
  --name-status strings — no real git invocation needed.

Scope

Only Bug 1. Two follow-up PRs cover Bugs 2 (inbound-edge pruning) and
3 (importMap recovery on rename) independently — they have no
overlap with the change-detection path touched here.

Marked Refs #366 rather than Closes #366 since two of the three
bugs ship in separate PRs.

Test plan

• pnpm test — 216 tests pass (200 prior + 16 new).
• pnpm lint — clean.
• Reviewer repro: baseline-scan a repo, git mv docs/a.md docs/b.md,
  commit, run /understand (incremental). Confirm the resulting
  graph contains only document:docs/b.md, not the stale
  document:docs/a.md node + its edges.

Refs #366

🤖 Generated with Claude Code