Cloud session checks out stale local branch when a commit is pushed between container pre-warm and session start

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

A Claude Code on the web session (started from the desktop app) came up one commit behind the remote tip of the branch I named. Reflogs show the harness did re-fetch the branch at session start and got the new tip (HEAD detached on it), then ran git checkout <branch>, which resolved to the local branch created ~9 min earlier during container pre-warm — pointing at the old tip. In the same second refs/remotes/origin/<branch> was rewritten back to the OLD sha, so git status reported up to date. SessionStart hooks then ran against the stale checkout, so a hook fix pushed minutes earlier had no effect.

Window: any push landing between container preparation (09:03) and session start (09:12) is silently dropped from the checkout.

What Should Happen?

HEAD is at the remote tip of the requested branch as of session start, and SessionStart hooks / CLAUDE.md / settings are read from that tip. If a local branch already exists from pre-warm, it should be forced onto the fetched tip (git checkout -B <branch> FETCH_HEAD or reset --hard origin/<branch>), and the remote-tracking ref must never be written back to a stale sha.

Error Messages/Logs

# all UTC. Missing commit bb04b761c pushed 09:11:22.
$ git reflog --date=iso
13513f9a8 HEAD@{09:12:59}: checkout: moving from bb04b761c to rainer/pr-body-shape-hook
bb04b761c HEAD@{09:12:55}:
13513f9a8 HEAD@{09:03:53}: checkout: moving from 13513f9a8 to rainer/pr-body-shape-hook
13513f9a8 HEAD@{09:03:42}:

$ git reflog show rainer/pr-body-shape-hook      # local branch never moved
13513f9a8 @{09:03:53}: branch: Created from refs/remotes/origin/rainer/pr-body-shape-hook

$ git reflog show origin/rainer/pr-body-shape-hook
bb04b761c @{09:18:43}: fetch -q origin rainer/pr-body-shape-hook: fast-forward   # my manual fetch
13513f9a8 @{09:12:59}:                                                            # rewritten to OLD sha, empty msg
bb04b761c @{09:12:55}: fetch --no-progress --depth 50 origin refs/heads/rainer/pr-body-shape-hook: fast-forward
13513f9a8 @{09:03:42}: fetch --no-progress --depth 50 origin refs/heads/rainer/pr-body-shape-hook: storing head

# mtimes: .git/refs/heads/<branch>=09:03:53  .git/shallow=09:12:46  .git/HEAD=09:12:59
# diag log: SessionStart hook_spawn_started at 09:13:05 (after stale checkout)

Steps to Reproduce

1. From the desktop app, start a cloud session on branch X of a repo. The container is prepared some minutes before the first turn.
2. Push a new commit to X during that gap.
3. In the session run git log -1, then git fetch origin X && git status -sb.

Result: HEAD is the pre-warm-time tip; status is "up to date" until the manual fetch, then [behind 1].

Claude Model

_No response_

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.42

Platform

Other

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Env: CLAUDE_CODE_ENTRYPOINT=remote_desktop, CLAUDE_CODE_REMOTE_ENVIRONMENT_TYPE=cloud_default, runner release-ba76006550-ext, CLAUDE_CODE_WORKER_EPOCH=1, git 2.43.0, shallow clone (--depth 50), private org repo.

Impact: work is based on an outdated tip (later non-ff push or silent revert of the missing commit); SessionStart hooks/settings come from the old commit; the stale remote-tracking ref hides it from git status.

Related, not duplicates: #55861 (web session never fetches before branching — here it fetched and then discarded the result), #41885 (marketplace sync fetches but never fast-forwards — same class, different path), #60295 (concurrent local sessions).