fix: detect edge index changes by ref object ID

[mparrett]

Why

ensure_edge_index_current refreshes the derived dependency graph at refs/notes/dep-graph before deps, ready, and topo run. It decides which issues to re-parse by comparing each note ref's commit date against a last_rebuilt_from marker.

e98395e fixed the timezone half of that comparison. The remaining problem is that a commit date does not say when a ref changed locally. A note arriving by fetch or import keeps the date it was written with, which can predate the marker, so its dependency headers are skipped permanently. hooks/post-merge fetches issue notes on every pull, so this is the ordinary sync path rather than a corner case. Reproduced on current main, with a backdated commit standing in for a fetched note:

$ git issue dep rebuild
$ GIT_COMMITTER_DATE=2020-01-01T00:00:00Z git issue update <c> --relates-to=<b>
$ git issue show <c> | grep '^relates_to'
relates_to: <b>
$ git issue deps
No dependency edges found.

A date cursor also never notices a ref that disappears, so a deleted issue's edges stay in the index until dep rebuild.

What

Snapshot issue ref object IDs in a refs blob beside the existing edges blob, and re-parse the refs whose ID moved. An object ID changes whenever a ref does, however it moved and whatever date it carries. Refs that have disappeared have their edges dropped.

The snapshot lives in a sibling blob rather than in the edges text, so existing readers of the index are unaffected. An index with no snapshot reads as "everything changed" and rebuilds in full, so an existing index heals on first read and there is no migration step.

Verification

Two regression tests in tests/test_deps.sh: a backdated header edit, and a deleted note ref. Both fail on main and pass on this branch. The shell suites under make test-all pass; the Emacs suite was not run.

Rebased onto b823d9c. The earlier TZ-pinned test is dropped, since e98395e covers that case.

🤖 Generated with Claude Code

[mparrett]

@nnunley Thanks again for sharing your project. I have a few bug fixes if you're interested. This is the first.

[nnunley]

Awesome. Glad you're trying it out and finding gaps.

[mparrett]

@nnunley I rebased this onto current main. You fixed the timezone part in e98395e, so I narrowed the PR to the remaining:

Notes that come in through a pull keep their original commit date. If that date is earlier than the index's last refresh, the dependencies in those notes never reach deps/ready/topo.

For example: a teammate adds X blocks Y, you pull, and Y still shows as ready. The fix here tracks note object IDs instead of dates, and it also drops edges for deleted issues. Repro and tests are in the description.Let me know if you'd prefer to solve this differently.