Bundle transport fails with 'refusing to merge unrelated histories' in shallow checkout

[mrjf]

Problem

The bundle transport for push_to_pull_request_branch (#30287) fails in the safe_outputs job because the job uses a shallow checkout (fetch-depth: 1). When git merge --ff-only tries to merge the bundle ref into the local branch, git refuses because the shallow clone doesn't have enough history to find a common ancestor.

[command]/usr/bin/git merge --ff-only refs/bundles/push-autoloop-build-tsb-pandas-typescript-migration
fatal: refusing to merge unrelated histories
##[error]Failed to apply bundle: The process '/usr/bin/git' failed with exit code 128

Reproduction

Every autoloop run on githubnext/tsessebe hits this. The safe_outputs job:

1. Shallow-clones main (fetch-depth: 1)
2. Fetches the PR branch (git fetch origin autoloop/build-tsb-pandas-typescript-migration)
3. Fetches the bundle to refs/bundles/...
4. Tries git merge --ff-only refs/bundles/... → fails: unrelated histories

The bundle contains commits that descend from the PR branch, but the shallow clone doesn't have enough history to see that relationship.

Possible fixes

1. Unshallow before merge: git fetch --unshallow (or deepen enough to find the merge base)
2. Use git update-ref instead of git merge --ff-only — directly point the branch at the bundle's HEAD (if the bundle is a strict superset)
3. Use the GitHub API to update the branch ref instead of local git operations
4. Increase fetch-depth in the safe_outputs checkout step

Impact

All autoloop programs on githubnext/tsessebe are blocked. Every run since the v0.72.1 upgrade fails at safe_outputs with this error.

Related

• Auto-switch push_to_pull_request_branch to bundle transport when merge commits are detected #30287 — introduced bundle transport (auto-switch when merge commits detected)
• push_to_pull_request_branch cannot handle merge commits — blocks long-running branch workflows #30286 — original merge commit handling issue