Checkpoints v2: Fix issue where migrations didn't check archived v2 transcripts

[computermode]

https://entire.io/gh/entireio/cli/trails/267

Fixes a bug where the migration repair path checked only v2/full/current to decide whether a migrated checkpoint still had its raw transcript. If that transcript had already been rotated into an archived ref like v2/full/0000000000001, rerunning the migration treated it as missing and copied old historical data back into current. That made current exceed the rotation threshold, so each later checkpoint/push kept creating more bogus archived generations.

1. Migration wrote/rotated some v2 full artifacts into archived refs like v2/full/0000000000001.
2. Migration was rerun.
3. The repair path checked only v2/full/current, did not see the archived raw transcript, and copied old checkpoint data back into current.
4. That made current look full of historical checkpoints, so later writes kept tripping the generation threshold and producing 0000000000002, 0000000000003, etc.

Pre-fix:

➜  gitsync git:(test-checkpoints-v2) git push origin HEAD
[entire] Pushing v2/main to origin....
[entire] Syncing v2/main with remote..... done
[entire] Pushing v2/main to origin.... done
[entire] Pushing v2/full/current to origin...
[entire] Syncing v2/full/current with remote............... done
[entire] Pushing v2/full/current to origin... already up-to-date
[entire] Pushing v2/full/0000000000008 to origin... already up-to-date

Post-fix:

➜  gitsync git:(test-checkpoints-v2) git push origin HEAD
[entire] Pushing v2/main to origin.... done
[entire] Pushing v2/full/current to origin.... done
Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 10 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 343 bytes | 343.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0), pack-reused 0 (from 0)
remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
To https://github.com/entireio/gitsync.git
   a0b43db..5b29a9b  HEAD -> test-checkpoints-v2

---

Note

Medium Risk
Touches git-ref selection and rotation behavior for v2 checkpoint transcripts plus migration repair heuristics; mistakes could write transcripts to the wrong generation or skip needed repairs, affecting checkpoint integrity.

Overview
Fixes v2 checkpoint finalization/repair logic to avoid rewriting /full/current when the raw transcript already lives in an archived /full/* generation (preventing repeated rotations and “rehydrating” old checkpoints back into current).

Adds /full/* artifact discovery (HasFullSessionArtifacts) and updates UpdateCommitted/migration repair to use it, including writing finalized transcripts back to the archived generation where they belong and factoring rotation checks into rotateCurrentIfNeeded (only triggered when /full/current is updated). Push migration hinting is also tightened to ignore malformed v1 checkpoint entries so the CLI doesn’t suggest migration when only broken v1 data is present; tests are updated/added to cover these cases.

^{Reviewed by Cursor Bugbot for commit 53e6b10. Configure here.}

[Copilot]

Pull request overview

Fixes a post-migration v2 checkpointing issue where repos with enough checkpoints to trigger rotation would repeatedly create new /full/<generation> rotations on subsequent pushes by ensuring “finalization” updates and repair checks don’t unnecessarily rehydrate data into /full/current.

Changes:

• Update v2 full-transcript finalization to write to the existing /full/* ref where the session’s artifacts live (current or archived), and rotate only when writing to /full/current.
• Adjust migration “repair” logic to treat archived /full/* artifacts as satisfying required full artifacts (avoids copying them back into /full/current).
• Add/adjust tests covering malformed v1 checkpoints, migration reruns with archived artifacts, and updating archived generations.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/push_common.go	Suppresses v2 migration hint when “missing” v1 entries are malformed (no readable summary).
cmd/entire/cli/strategy/push_common_test.go	Adds a malformed v1 checkpoint helper + test to validate hint suppression behavior.
cmd/entire/cli/migrate.go	Uses v2 store’s /full/* artifact check during repair (instead of /full/current only).
cmd/entire/cli/migrate_test.go	Updates migration test expectations and adds a helper to assert /full/current stays unrehydrated.
cmd/entire/cli/checkpoint/v2_committed.go	Adds /full/* artifact discovery and updates full transcript finalization to target archived refs when appropriate; refactors rotation check.
cmd/entire/cli/checkpoint/v2_generation_test.go	Adds coverage ensuring UpdateCommitted updates archived generations without repopulating /full/current.