fix(pr-branch): sub_repos from config silently ignored — git commands run on root repo

[fleizean]

Bug Description

/gsd:pr-branch ignores sub-repos defined in planning.sub_repos config. All git commands inside the sub-repo handling path run without a -C <repo> flag, so they operate on the shell's current working directory (the root repo) instead of the intended sub-repo.

Steps to Reproduce

1. Set up a project with planning.sub_repos: ["backend", "frontend"] in .planning/config.json
2. Make uncommitted changes inside one of the sub-repos (e.g. backend/)
3. Run /gsd:pr-branch
4. Observe: sub-repos are never scanned; no PR is created for backend/

Expected Behavior

For each sub-repo in planning.sub_repos:

• git -C "$REPO" status --porcelain detects uncommitted changes
• User is prompted to handle all / select / skip
• Selected repos get a branch created, changes committed, pushed, and a companion PR opened

Actual Behavior

Sub-repos are silently skipped. Git commands were being called without -C <repo>, so they operated on the root repo's working directory.

Root Cause

The pr-branch workflow lacked a handle_sub_repos step. Git commands were not scoped with git -C <repo> — relying on cd which does not persist shell state between agent-executed commands.

Environment

• GSD Version: current next branch
• Runtime: Claude Code
• OS: macOS

[trek-e]

This was generated by AI during triage.

Triage: confirmed-bug

Confirmed against next (read-only code trace). gsd-core/workflows/pr-branch.md (157 lines) has no sub-repo handling whatsoever — grep for sub_repos, handle_sub, companion, and git -C all return nothing. Every git command in the workflow is bare and runs against the root repo's cwd. The command entry commands/gsd/pr-branch.md just delegates to the workflow and adds no sub-repo logic either.

The config key is real and actively consumed elsewhere, which is what makes the gap a genuine bug rather than a non-feature:

• planning.sub_repos is canonical in gsd-core/bin/shared/config-schema.manifest.json (default []).
• gsd-core/bin/lib/commands.cjs (groupFilesBySubrepo() / cmdCommitToSubrepo()) already scopes per sub-repo via path.join(cwd, repo) + execGit({ cwd: repoCwd }) — the correct pattern pr-branch is missing.
• Also consumed by gsd-core/bin/lib/core.cjs and gsd-core/agents/gsd-executor.md.

So commits can land in sub-repos, but pr-branch never scans them, never creates a filtered branch per sub-repo, and never opens companion PRs.

Note: the issue body is written in past tense ("git commands were being called without -C") as if a fix exists — it does not exist on next. The correct scoping precedent to follow is commands.cjs's { cwd: repoCwd }, since cd does not persist across agent-executed commands.

Labeling confirmed-bug, removing needs-triage.