Prune checkpoint refs

[aquamoth]

Current behaviour

Every turn writes a snapshot commit and a ref named
refs/t3/checkpoints/<base64 thread id>/turn/<n>. The refs are never
removed. Deleting or archiving a thread leaves its refs in place, and I
found no setting to turn checkpointing off.

In one repository, nine days of use produced 257 checkpoint refs across
16 threads. Most of those threads are finished and their branches are
merged and deleted.

Why it matters

The refs sit outside refs/heads, so git branch does not list them and
they are never pushed. Git GUIs are a different story. TortoiseGit's
revision graph walks every ref and shows each checkpoint as a labelled
node, and its log dialog shows them in "All refs" mode. After a few
weeks the graph is unreadable. Other tools that draw all refs will behave
the same way.

There is also a robustness angle: #10905 reports zero-byte checkpoint
ref files after an unclean restart. The more refs there are, the larger
that surface.

Today the only workaround is a manual git update-ref -d loop over
refs/t3/checkpoints, which also discards the revert history of threads
still in use.

Proposal

Any of these would solve it, in order of preference:

1. Delete a thread's checkpoint refs when the thread is deleted, and
   optionally when it is archived.
2. Add a retention setting, by age or by number of threads, with a
   "prune now" action in the project settings.
3. Add a setting to disable checkpointing for a project, for users who
   never use turn revert.

Related

• Clean up failed checkpoint writes #9808 covers debris from failed captures, not completed checkpoints.
• "Add supported retention and compaction for unbounded local SQLite
  growth" asks for the same kind of retention for the local database.
• feat(worktrees): manage lifecycle on orchestrator v2 #5589 deliberately keeps checkpoint refs when pruning worktrees so
  revival stays possible. A thread-deletion hook would not conflict with
  that, since a deleted thread has nothing left to revive.

Observed on T3 Code 0.0.42 on Windows 11 with TortoiseGit 2.19.1.

[aquamoth]

I wrote a fix in PR #13273

[stychu]

I've also hit this problem. This can pollute agent context when told to audit things @Bil0000 @juliusmarminge