[Bug]: Storage cleanup deletes git worktrees nested inside a thread worktree, including uncommitted work #23866

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. Use a project whose root is a git repo that gitignores a folder where another repo lives, for example /backend/ holding a separate backend clone. This is a common "workspace repo" layout: agent instructions and skills sit at the root, and the product repos are gitignored inside it.
2. Start a thread in a new worktree.
3. Inside that thread worktree, have the agent create a worktree of the other repo at the ignored path (git -C <root>/backend worktree add <thread-worktree>/backend -b fix/x), and leave an uncommitted file in it.
4. Leave the thread idle, with storage cleanup set to worktreeUnchanged: true (or delete the thread with worktreeOnDelete), and run storage cleanup.

A git-only repro of the underlying removal:

git init -q umb && printf '/backend/\n' > umb/.gitignore && git -C umb add . && git -C umb commit -qm base
git init -q be && touch be/f && git -C be add . && git -C be commit -qm base
git -C umb worktree add -q ../task -b task/x
git -C be worktree add -q ../task/backend -b fix/y
echo wip > task/backend/wip.txt
git -C task status --porcelain          # empty: backend/ is ignored
git -C umb worktree remove ../task      # succeeds; task/backend/wip.txt is gone
git -C be worktree list                 # task/backend is now "prunable"

Expected behavior

Cleanup keeps a worktree that contains another git worktree or repository, the same way it already keeps one that contains a project checkout.

Actual behavior

The nested worktree is deleted along with its uncommitted files, and the other repo is left with a stale (prunable) worktree entry. Its commits survive, because they're stored in the other repo.

Impact

Uncommitted work is lost silently. An umbrella worktree never gets commits of its own, so with worktreeUnchanged on it is cleaned up as soon as the thread is idle and its session has ended.

Cause (in apps/server/src/storageCleanup.ts):

• localChangesReason relies on git status, which doesn't report ignored paths.
• containsProjectRoot only protects checkouts of registered T3 projects.
• removeLinkedWorktree then runs git worktree remove, which deletes ignored nested repos recursively.
• With worktreeKeepWhen: "tracked-changes", the git clean -ffdx before removal also deletes nested repos (the double -f).

worktreeKeepWhen: "any-local-files" avoids it, but it isn't the default.

Suggested fix: before removing a worktree, refuse if it contains any .git file or folder other than its own at the root, or any path registered in another repo's git worktree list.

Version or commit

0.1.2-nightly.20261022.3541 (source read at 2c8bdf61)

Environment

Linux, git 2.53.0, Node 22.23.2, Claude Code 2.1.308

Logs or stack traces

None; the git-only repro above shows the removal.

Workaround

Keep other repos' worktrees outside T3's worktrees folder, or set worktreeKeepWhen: "any-local-files" for the project.