Repository with submodules fails to initialize session (`unexpected gitdir format`)

[pjbgf]

What happened?

When running a Claude session in a repository that contains Git submodules, the session fails to initialize with the following error:

● Ran 1 stop hook (ctrl+o to expand)
  ⎿  Stop hook error: Failed with non-blocking status code: 2026/03/06 12:52:26 INFO turn-end component=lifecycle agent=claude-code
  event=TurnEnd session_id=a4f4d879-7b82-472e-9e5f-290f1346089c
  session_ref=/home/coder/.claude/projects/-home-coder-git-go-git-entire/a4f4d879-7b82-472e-9e5f-290f1346089c.jsonl
  failed to save step: failed to initialize session: failed to get worktree ID: unexpected gitdir format (no worktrees): ../.git/modules/go-git

Repository Structure

The repository uses Git submodules and has a structure similar to:

/repo
    /submodule1
    /submodule2

The session is started and worked on at /repo level.

Steps to reproduce

No response

Entire CLI version

v0.4.9

OS and architecture

Tumbleweed amd64

Agent

Claude Code

Terminal

Alacritty

Logs / debug output

{"parentUuid":"ab348121-b962-4b90-8f17-8428552fb823","isSidechain":false,"userType":"external","cwd":"/home/coder/git/go-git/entire/go-git","sessionId":"a4f4d879-7b82-472e-9e5f-290f1346089c","version":"2.1.69","gitBranch":"filesystem-perf","slug":"adaptive-whistling-shell","type":"system","subtype":"stop_hook_summary","hookCount":1,"hookInfos":[{"command":"entire hooks claude-code stop","durationMs":194}],"hookErrors":["Failed with non-blocking status code: 2026/03/06 01:49:09 INFO turn-end component=lifecycle agent=claude-code event=TurnEnd session_id=a4f4d879-7b82-472e-9e5f-290f1346089c session_ref=/home/coder/.claude/projects/-home-coder-git-go-git-entire/a4f4d879-7b82-472e-9e5f-290f1346089c.jsonl\nfailed to save step: failed to initialize session: failed to get worktree ID: unexpected gitdir format (no worktrees): ../.git/modules/go-git"],"preventedContinuation":false,"stopReason":"","hasOutput":true,"level":"suggestion","timestamp":"2026-03-06T01:49:09.461Z","uuid":"b5af7a93-f458-4818-9cfe-0c17d01c8ef6","toolUseID":"43a47dfd-ae1e-47b1-8d34-ef069e8db9a3"}

Additional context

No response