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subprocess.run's timeout SIGKILLs only the direct git child, so the lock is left behind and git's helpers are orphaned. On a slow SD card the same pull then times out on every retry and recreates the lock, so removing it by hand does not help. - run_git starts git in its own session, stops the group with SIGTERM before SIGKILL, and clears the lock if nothing owns it. Update Code's pull, checkout, reset and stash go through it, with a 600s pull timeout. - Read-only calls (describe --dirty, status, the update-check fetch) set GIT_OPTIONAL_LOCKS=0 so a timed-out poll cannot take the lock. - A timed-out pull returns a clear error; a rebase left by an interrupted update is aborted before pulling. - The manual-fix hint says to stop the services and kill running git. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>