main 61c3794c32 after UI Revert files too
?? web/
web/node_modules/pkg/index.js
web/.env
baseline
keep-preexisting
keep-secret

original PR nested-repository failure from running server:
      '      [cause]: VcsProcessExitError: VCS process failed in GitVcsDriver.checkpoints.restoreCheckpoint: git clean (/home/user/t3code/.t3/worktrees/restore-hunt-pr/t3-ad2e2862) exited with 0 - Could not clean the checkpoint workspace: untracked files remain.\n' +

corrected head e7ac91124693daeb4e2f26fd9785ed7c554c3b21
after Revert files too, followed by Revert and keep changes:
git status --short:
 M tracked.txt
?? scratch/
test ! -e web:
PASS
preexisting.env / secrets.env / scratch/nested/private.txt / tracked.txt:
keep-preexisting
keep-secret
keep-nested
keep-changes
git diff --cached --name-only:

running app cleanup-limit failure observed
      '      [cause]: VcsProcessExitError: VCS process failed in GitVcsDriver.checkpoints.restoreCheckpoint: git clean (/home/user/t3code/.t3/worktrees/restore-hunt-pr/t3-818de98f) exited with 0 - Could not clean the checkpoint workspace: untracked files remain.\n' +
staged paths: ""
status:
?? checkpoint.txt
?? d/
checkpoint.txt: checkpoint
tracked.txt: baseline