[bug]Fix rewind of tracked checkpoint deletions

[stale2000]

Entire Logs: https://entire.io/gh/stale2000/cli/session/019eb3a9-4eee-7440-ac23-ca4fbe5cdd38

COMMENTS:

I'm having a difficult time wrapping my head around this bug, but the logs pretty clearly keep insisting that there is an issue. It might be better to use this as a guideline to implement a fix because I don't really understand how the fix works.

What was broken

entire rewind is supposed to make the working tree match the selected checkpoint. Checkpoint trees represent deleted files the same way Git trees do: the deleted path is simply absent from the tree.

Before this change, rewind only deleted extra untracked files and then restored files that were present in the checkpoint tree. It did not remove tracked files that were present in the current branch HEAD but absent from the checkpoint. That could leave stale files on disk after rewind.

Concrete example

Start with the current branch containing two tracked files:

HEAD / working tree before rewind
├── keep.txt
└── delete-me.txt

The selected checkpoint represents this state:

checkpoint tree
└── keep.txt

delete-me.txt is not in the checkpoint because it had been deleted when the checkpoint was created.

Old behavior after rewind:

working tree after rewind, before this fix
├── keep.txt        restored correctly
└── delete-me.txt   BUG: stale tracked file remained

New behavior after rewind:

working tree after rewind, with this fix
└── keep.txt

Why deletion is safe here

This does not blindly delete arbitrary files. The new deletion pass is scoped to files that are:

• tracked by the current HEAD commit, meaning the current branch commit contains that path
• absent from the selected checkpoint tree
• outside protected paths such as .git, .entire, and agent config directories

Existing untracked-file protections still apply. Untracked files that existed at session start are preserved, and ignored directories are not walked.

What changed

• Rewind now compares tracked HEAD paths with the selected checkpoint tree before restoring present files.
• Tracked files missing from the checkpoint are removed from the working tree.
• PreviewRewind reports those tracked deletions so interactive users can see the files that will be removed.
• Added a regression test for a checkpoint that deletes a tracked file.

Verification

• mise run lint
• go test ./cmd/entire/cli/strategy -run 'TestShadowStrategy_(PreviewRewind|Rewind_)' -count=1
• go test ./cmd/entire/cli/strategy ./cmd/entire/cli/checkpoint

Notes

Full mise run check was attempted, but currently fails in unrelated date-sensitive test TestRunAuthStatus_RendersSessionsTable: expected 2026-01-01, output rendered 2026-01-31. Strategy/checkpoint tests passed during that run.