Fix apply_samples cross-repo subdirectory patch staging (#40086)

[dsyme]

Summary

Fixes #40086. After #40080 unmasked it, gh aw compile --use-samples replay
fails with Failed to pin branch '...': ERR_SYSTEM: fatal: Needed a single revision
when a create_pull_request / push_to_pull_request_branch sample patch targets
a cross-repo checkout placed in a subdirectory (path: github).

Root cause

apply_samples.cjs's preStagePatch always created the sample branch and
committed the patch in the main workspace root (GITHUB_WORKSPACE). For a
cross-repo checkout in a subdirectory, the safe-outputs MCP handler resolves the
target repo to ${GITHUB_WORKSPACE}/github via the checkout manifest and looks
for the branch there — but the branch was created in the root, so pinning failed.

Fix

apply_samples.cjs:

• readConfiguredTargetRepo(tool) — reads the per-tool target-repo from the
  safe-outputs config (GH_AW_SAFE_OUTPUTS_CONFIG_PATH).
• resolvePatchWorkspace(entry, workspace) — resolves the on-disk checkout
  directory for the target repo using the same manifest-first findRepoCheckout
  the MCP handler uses (target repo from the sample's arguments.repo override or
  the configured target-repo). Falls back to the workspace root when no target
  repo is set or the checkout can't be located.
• preStagePatch now stages the branch/commit in that resolved directory instead
  of always the root.

Tests

• Added a regression test reproducing the path: github side-repo layout,
  asserting the branch/commit/file land in the subdirectory and not the main
  repo root.

Validation

• All JS tests pass (23 in apply_samples.test.cjs), typecheck + prettier pass.
• Go samples-replay tests pass; the driver bundles cleanly with the new dependency.

[github-actions]

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Generated by 🧪 Smoke CI for issue #40087 · ◷

[Copilot]

Pull request overview

This pull request fixes gh aw compile --use-samples replay failures when a create_pull_request / push_to_pull_request_branch sample patch targets a cross-repo checkout located in a workspace subdirectory (e.g. path: github). It does so by resolving the correct on-disk checkout directory (via the checkout manifest) and staging the sample branch + commit in that checkout instead of always using the workspace root.

Changes:

• Add readConfiguredTargetRepo() and resolvePatchWorkspace() to determine the correct repo checkout directory for staging sample patches.
• Update preStagePatch() to run all git operations in the resolved checkout directory.
• Add a regression test covering cross-repo subdirectory layouts and a changeset entry.

Show a summary per file

File	Description
actions/setup/js/apply_samples.cjs	Resolve target checkout directory for patch staging and stage branches/commits in that repo directory.
actions/setup/js/apply_samples.test.cjs	Add regression test ensuring branches/commits/files land in the subdirectory checkout, not the workspace root.
.changeset/patch-apply-samples-cross-repo-subdir-staging.md	Document the patch-level fix in release notes.

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• Files reviewed: 3/3 changed files
• Comments generated: 1