[Bug]: After a thread moves to another worktree, its next turn's diff shows the other branch, and "Revert files too" overwrites the new worktree with the old one's files #30876

Before submitting

• I searched existing issues and did not find a duplicate.
• I included enough detail to reproduce or investigate the problem.

Area

apps/server

Steps to reproduce

1. Start a thread in worktree A of a repository and send a turn that edits a file.
2. Move the thread to worktree B of the same repository, on another branch with its own commits and files.
3. Send a turn that edits one file.
4. Open turn 2's diff.
5. Choose "Edit from here?" on turn 1, then "Revert files too".

Expected behavior

• Turn 2's diff lists only the file turn 2 edited.
• A file revert never writes a checkpoint taken in one worktree into another. It is refused, and the conversation-only revert still works.

Actual behavior

• Turn 2's diff lists every difference between A's tree and B's tree (B's branch commits and turn 1's files) as turn 2's changes.
• The revert is accepted and writes A's turn-1 tree into worktree B, so B's branch-only files are deleted or reverted.
• With B in another repository instead, turn 2's baseline is missing and its diff is empty or wrong.

Impact: data loss in the destination worktree (uncommitted and branch-only files) from an action the UI presents as safe.

Why, in the current code:

• CheckpointService.makeRootRunScope allocates every root run's scope from the one name ROOT_CHECKPOINT_SCOPE_NAME ("root"), and writes the run's own cwd into it. A thread therefore has one root checkpoint scope, re-created by each run with that run's cwd.
• Checkpoint refs are per scope and ordinal and live in the repository, which worktrees of one repository share. So turn 2 is diffed against the ref A's turn 1 left.
• isCheckpointRestoreIsolated (CheckpointRestoreSafety.ts) compares the scope's cwd (now B) with the thread's worktreePath (B), so the check passes.

Related but different: #27336 reports the same diff symptom when the agent moves into a worktree of its own or switches branch, without T3 Code moving the thread.

Impact

Major degradation or frequent failure

Version or commit

main @ 8b44f42

Environment

No response

Logs or stack traces

No response

Screenshots, recordings, or supporting files

No response

Workaround

Use the conversation-only revert, not "Revert files too", on turns taken before the thread moved to another worktree.

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