Summary

When git worktree add creates a new worktree from a monorepo that uses git submodules, the submodule directories in the new worktree are empty. Archon does not run git submodule update --init after worktree creation, so any workflow that needs to operate on submodule content will find empty directories.

Root Cause

WorktreeProvider.createWorktree() (packages/isolation/src/providers/worktree.ts) calls git worktree add without --recurse-submodules, and no git submodule update --init is run afterward. Git's default worktree add behavior creates the .gitmodules file but leaves submodule directories empty.

Expected Behavior

After worktree creation, submodules should be initialized and checked out so that workflows can operate on the full monorepo content.

Suggested Fix

After git worktree add succeeds in createNewBranch(), run:

git -C <worktreePath> submodule update --init --recursive

This should be conditional — only when the repo has a .gitmodules file — to avoid unnecessary overhead for repos without submodules. Consider making it configurable via .archon/config.yaml (worktree.initSubmodules: true/false).

Related

• Worktree reuse matches environments from different local clones of the same remote #1183 — worktree reuse across different local clones (fixed in fix: prevent worktree reuse across different local clones #1186)
• Parallel workflow collision in shared worktree paths (see below)

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