Codex Desktop caches stale large-diff result after bad empty-tree snapshot is removed

What version of the Codex App are you using (From “About Codex” dialog)?

26.417.41555

What subscription do you have?

Pro $200

What platform is your computer?

Microsoft Windows NT 10.0.22631.0 x64

What issue are you seeing?

Codex Desktop review/diff pane appears to cache a stale large-diff result and keeps showing whole-repo deletion behavior even after the underlying Git state has been corrected.

The app shows:

Large diff detected -- showing one file at a time

The app appears to think the branch deletes the whole repository. Git itself does not agree.

Local Git consistently reports the real branch diff as small:

git diff --shortstat master...HEAD

Output:

39 files changed, 2210 insertions(+), 27 deletions(-)

GitHub also does not show the huge diff.

What I Tried
I verified the branch and commits directly with:

git status --short --branch
git merge-base master HEAD
git diff --shortstat master...HEAD
git diff --name-status master...HEAD
git cat-file -p <commit>
git diff-tree --stat --summary <parent> <commit>
The rebuilt branch is based directly on master, and the two commits are normal:

673c48b3 SLW-1161 Initial version of federal criminal check
7e58cfd0 Remove reference to 15 year sex offender in scope message
The first commit’s parent is exactly local master:

parent cabedee31dbf5384283141566d9edb5cef389d3d

The merge base is also exactly master:

git merge-base master HEAD

Output:

cabedee31dbf5384283141566d9edb5cef389d3d

I also rebuilt the branch from scratch:

Checked out master.
Created a new branch.
Cherry-picked the two commits.
Verified the diff again.
The app still showed the huge diff.

Suspicious Local Findings
There had been a stale Codex snapshot ref:

refs/codex/snapshots/45325e75ddf31537ae8f7aa7dadd82fab0559c85

It pointed to:

8aa91d72 Codex worktree snapshot: archive-cleanup

That commit had Git’s empty tree:

tree 4b825dc642cb6eb9a060e54bf8d69288fbee4904

Comparing master to that object produced the exact huge deletion diff:

git diff --shortstat master..8aa91d72512643fd29a2d93aa8828d1023fdcdc7

Output:

1782 files changed, 424540 deletions(-)

I deleted the stale refs/codex/snapshots/... ref and quarantined the unreachable loose object. After that:

git cat-file -e 8aa91d72512643fd29a2d93aa8828d1023fdcdc7

Now fails, meaning Git can no longer resolve that bad object.

The app still showed the large-diff mode.

I also found stale .git/info/refs contents advertising old branch SHAs. I regenerated it with:

git update-server-info

Afterward .git/info/refs matched real refs, but Codex Desktop still showed the huge diff.

Expected Behavior
Codex Desktop review/diff pane should invalidate stale diff/cache state when refs or underlying Git objects change.

It should match Git:

git diff --shortstat master...HEAD

Output:

39 files changed, 2210 insertions(+), 27 deletions(-)

It should not continue showing large-diff mode or whole-repo deletion behavior after the bad snapshot ref/object has been removed.

Actual Behavior
Codex Desktop continues to show:

Large diff detected -- showing one file at a time

This still happens after:

deleting the stale Codex snapshot ref,
removing the bad empty-tree object,
regenerating .git/info/refs,
restarting Codex Desktop,
opening a new thread,
creating a new branch at the same commit,
creating a fresh branch from master and cherry-picking the commits.
Why This Seems Like a Cache Bug
The commits and refs are normal according to Git. The only object that produced the app’s huge diff was an old Codex empty-tree snapshot object. Even after that object became unreachable and then unresolvable, the app appears to retain or recompute the same invalid large diff.

This looks like stale review/diff cache state or a bad cached branch-base/snapshot selection in Codex Desktop.

What steps can reproduce the bug?

Uploaded thread: 019d6445-900c-7ef2-b019-29844177e746

Frankly, I'm not sure. At one point I think I manually deleted a worktree -- bad idea I know -- but it should not have a caused this. The git branch in its real state is fine.

What is the expected behavior?

The diff pane which shows the difference from master should show only the 2 new commits, with about 39 files. It should not show 400k lines deleted (basically the entire repo).

Additional information

My repo is in WSL. CODEX_HOME points to a directory under Windows.