msd-core/docs/how-to/fix-worktree-base-mismatch.md

How to fix the worktree base-mismatch (exit 42) error

Goal: Understand why /gsd-execute-phase halts with FATAL: worktree base mismatch / exit 42 when your branch is ahead of the default branch, and choose the right fix to restore normal — or parallel — execution.

Prerequisites: GSD Core is installed and you have an active project. You have run /gsd-execute-phase and either seen the exit-42 error or the one-line ⚠ Worktree base mismatch warning.

---

What you will see

When you run /gsd-execute-phase on a branch that is ahead of the repository's default branch (for example, an unmerged milestone branch, a long-lived feature branch, or a branch with commits not yet in origin/HEAD), you may see one of two messages:

Automatic-degrade warning (phase still completes):

⚠ Worktree base mismatch: HEAD (abc12345) differs from origin/HEAD (def67890).
Running this phase sequentially on the main working tree.
To keep parallel worktrees, set worktree.baseRef:"head" in
.claude/settings.local.json (or run: gsd-tools worktree set-baseref). See #683.

The phase runs to completion sequentially; nothing is blocked. This is the runtime mitigation.

Exit-42 halt (older installs or misconfigured environments):

FATAL: worktree base mismatch

All worktree-isolated executors halt immediately. Zero progress is made.

---

Why this happens

Claude Code's isolation="worktree" forks executor worktrees from the repository's default branch (origin/HEAD), not from your current HEAD. When your branch contains commits that origin/HEAD does not have — plan files, new source files, anything added since the branch diverged — those files are absent inside each worktree. GSD's worktree-branch-check safety guard correctly refuses to act on a worktree that does not match the orchestrator's state, and exits with code 42.

This is the guard working as designed: it prevents silent data loss or phantom edits in the wrong tree. The error is a branch-state condition, not an OS-specific or hardware issue.

---

Option 1 — Do nothing (you are already unblocked)

If you saw the ⚠ Worktree base mismatch warning rather than an exit-42 halt, GSD has already automatically degraded to sequential execution on the main working tree for this run. The phase will complete. No action is required.

Use this option when:

• You are on a diverged branch temporarily
• You do not care about parallel execution for this phase
• You want to merge back to the default branch soon

---

Option 2 — Permanent fix: set worktree.baseRef: "head" (recommended)

This option restores parallel worktree execution on diverged branches. It tells Claude Code to fork executor worktrees from your current HEAD instead of origin/HEAD, so the plan files and branch-only commits are present in every worktree.

Run the convenience command from your project root:

node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" worktree set-baseref

This writes worktree.baseRef: "head" into .claude/settings.local.json in your project root. It is no-clobber: if you already have an explicit baseRef set to something else, it leaves your value in place and tells you.

To verify the result:

node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" worktree base-check

The output is JSON. When shouldDegrade is false and reason is "baseref-head", parallel worktrees will work on any branch.

Alternatively, set the value by hand in .claude/settings.local.json:

{
  "worktree": {
    "baseRef": "head"
  }
}

Note: Fresh installs and upgrades of GSD Core both set worktree.baseRef:"head" automatically in .claude/settings.local.json (no-clobber) when workflow.use_worktrees is enabled (the default). You can also apply or re-apply it manually at any time with gsd-tools worktree set-baseref — for example, if you toggled worktrees on after the initial install.

Use this option when:

• You regularly work on long-lived or milestone branches
• You want parallel phase execution (faster, lower context-window pressure)
• You are a solo developer or team working on a feature branch for an extended period

---

Option 3 — Fallback: disable worktrees entirely

If worktrees are causing persistent problems beyond the base-mismatch (for example, your environment does not support them), disable them permanently for this project:

Add or edit .planning/config.json:

{
  "workflow": {
    "use_worktrees": false
  }
}

All executor agents will then run sequentially on the main working tree for every phase. This is equivalent to what the automatic degrade does, but permanent.

Use this option when:

• Worktrees are consistently problematic in your environment
• You prefer sequential execution for auditability or tooling reasons
• You are on a platform or CI setup that does not support git worktrees

See also: workflow.use_worktrees in the configuration reference.

---

The exit-42 backstop

The worktree-branch-check guard (exit 42) remains active in all execution modes as a safety backstop. It fires only when an executor worktree's branch does not match the expected orchestrator state — a condition that should not arise once you have applied one of the options above. If you continue to see exit 42 after setting worktree.baseRef: "head", run /gsd-forensics to investigate.

---

Summary

Situation	Recommended action
Saw the warning, phase completed	Nothing — degrade handled it automatically
Regularly on diverged branches, want parallel execution	worktree set-baseref (Option 2)
Worktrees consistently problematic	Set workflow.use_worktrees: false (Option 3)
Still seeing exit 42 after fixes	Run /gsd-forensics "exit 42 after fix"

---

Related

• Recover and troubleshoot
• Debug a failed execution
• Configuration reference — workflow toggles
• CLI Tools reference — worktree commands
• docs index