apply_samples: create_pull_request bundle includes stray runtime files (.local/state/gh/device-id)

[dsyme]

Summary

When the apply_samples driver replays a create_pull_request sample inside the agent job, the resulting bundle / patch contains files that were not declared in the sample patch — specifically host runtime artefacts such as .local/state/gh/device-id that get written into the workspace by the gh CLI during agent setup.

These extra files trigger protected_files_policy: request_review in the safe-outputs handler, so the safe-outputs job creates a fallback issue instead of the intended pull request, and the workflow exits successfully with no PR.

Reproduction

• Repo: githubnext/gh-aw-test
• Workflow: test-copilot-siderepo-create-pull-request.md
• Run: https://github.com/githubnext/gh-aw-test/actions/runs/27276691700

Evidence

safe_outputs job log:

Processing create_pull_request: title=Multi-commit test from Copilot, ...
Patch file path: /tmp/gh-aw/aw-githubnext-gh-aw-side-repo-gh-aw-sample-copilot-siderepo-multi-commit.patch
...
##[warning]Protected file protection triggered (request_review): .local/state/gh/device-id. Will create pull request with caution and request-changes review.
...
git diff-tree -r --raw <commit-sha>
:000000 100644 0000... cac197... A .local/state/gh/device-id
:000000 100644 0000... 75b21f... A README-test.md
...
##[error]Git push failed: pushSignedCommits: refusing unsigned push for branch '...': Signed-commit payload violates file-protection policy (request_review): .local/state/gh/device-id
##[warning]Git push operation failed - creating fallback issue instead of pull request
Created fallback issue #152: https://github.com/githubnext/gh-aw-side-repo/issues/152

The sample patch only declares README-test.md. apply_samples likely uses git add -A (or equivalent) when staging the sample commit, picking up workspace pollution.

Suggested fix

apply_samples should stage only the files declared in the sample patch (e.g. git apply --index <patch> or apply + diff-list-then-add), never git add -A. That way runtime artefacts placed in the workspace by other actions don't leak into sample bundles.

Impact

• Every siderepo create-pull-request sample currently fails to actually create the PR. The workflow exits successfully so this is silent.
• Filing as a follow-up to samples mode: create_pull_request fails with ERR_SYSTEM merge-base for siderepo workflows #37836 — a different root cause but the same end-to-end symptom (siderepo create-pull-request samples don't produce PRs).