/resume in worktree containers is orphaned: Claude Code keys transcripts by raw CWD path, so worktree sessions are invisible from the main repo (and vice versa)

[schmitthub]

Related: #368 (same family — worktree topology breaking tooling that resolves identity through git).

Symptom

/resume inside a clawker worktree container cannot see past conversations from the repository. Worktree-session chats are likewise invisible from the main checkout. Worktree sessions end up orphaned and isolated from the root repository's history.

Mechanism (observed live from inside a worktree agent container, 2026-06-10)

Claude Code stores conversation transcripts under ~/.claude/projects/<flattened-cwd-path>/*.jsonl — keyed by the raw working directory path, not the git repository. In the agent's config volume right now:

• ~/.claude/projects/-Users-andrew-Code-clawker/ — main-checkout sessions
• 22 separate sibling dirs of the form -Users-andrew-Code-clawker--clawkerlocal--local-share-clawker-worktrees-clawker-clawker-<id>/ — one per worktree container that ever ran, each holding that worktree's transcripts

The active session's transcript is being written to the worktree-keyed dir, not the main one. Since /resume lists sessions for the current project dir:

• in a worktree container, it shows only that worktree path's sessions — no repo history;
• in the main checkout, worktree sessions never appear;
• worktree paths are unique per branch and deleted on worktree remove, so those transcript dirs become permanently unreachable garbage.

The split-brain that proves linkage is possible

Claude Code's file-based auto-memory for this same session resolves to the MAIN repo's project dir (~/.claude/projects/-Users-andrew-Code-clawker/memory/) even though CWD is the worktree — so some CC subsystem already maps worktree → main repo (presumably via git common-dir resolution; git rev-parse --git-common-dir from the worktree works in-container and returns the main .git). Transcript keying just doesn't use that mapping. Whether that's upstream CC behavior or something our mount/ownership layout degrades is the open question.

Discriminating tests (not yet run)

1. Host-side control: open CC in a plain git worktree on the host (no clawker) and run /resume — if main-repo sessions are also invisible there, this is upstream CC behavior, not clawker breakage → becomes a CC feature request + clawker-side mitigation.
2. Production-layout container: verify git rev-parse --git-common-dir works in a production worktree container (worktrees in the XDG data dir; main repo top-level is root-owned scaffold — the Go -buildvcs cannot stamp linked worktrees: wrong-parent stamping, dubious-ownership failures, and the scope of the GOFLAGS mitigation #368 dubious-ownership guardrail might block discovery there even if the dev .clawkerlocal layout works).
3. Confirm whether /resume within the SAME worktree+agent across container restarts works (same path + persistent config volume ⇒ should), to scope the report precisely.

Candidate clawker-side mitigations (sketch)

• At container init (or in the workspace/containerfs layer), pre-create ~/.claude/projects/<flattened-worktree-path> as a symlink to the main repo's project dir, so worktree sessions read/write the shared history. Needs care: the flattening scheme is CC-internal (path with / and . → -), so this couples to an undocumented convention — verify against the observed dirs and gate on it.
• Alternatively keep per-worktree isolation but garbage-collect/migrate transcript dirs on clawker worktree remove so history isn't silently orphaned.
• If host-side CC turns out to link worktrees correctly (test 1) and only our containers don't, diff what resolution input is missing in-container (ownership, mount set, env) and fix that instead.

Evidence commands

# inside a worktree agent container
ls ~/.claude/projects/                       # main dir + one dir per worktree path
ls -lt ~/.claude/projects/*/*.jsonl | head   # active transcript lands in the worktree-keyed dir
git rev-parse --git-common-dir               # main .git — resolution input exists

🤖 Generated with Claude Code