push_to_pull_request_branch cannot handle merge commits — blocks long-running branch workflows

[mrjf]

Problem

When an agent merges the default branch into a PR branch locally (to stay up-to-date), the resulting push_to_pull_request_branch patch includes the merge commit. git am --3way cannot apply merge commits, so the push fails with add/add conflicts even though the agent resolved them locally.

This completely blocks long-running branch workflows like autoloop, where the branch accumulates iterations over time and must periodically merge main.

Reproduction

1. A long-running PR branch (autoloop/tsb-perf-evolve) is 6 ahead, 22 behind main
2. Both the branch and main have src/stats/hash_pandas_object.ts (added independently)
3. The agent checks out the branch, merges main (resolving the add/add conflict locally), commits new work
4. The agent calls push_to_pull_request_branch
5. The incremental patch (git format-patch origin/branch..branch) includes the merge commit
6. git am --3way fails:

   CONFLICT (add/add): Merge conflict in src/stats/hash_pandas_object.ts
   CONFLICT (add/add): Merge conflict in tests/stats/hash_pandas_object.test.ts
   Failed to apply patch
   

Why this keeps happening

The agent cannot push directly — git credentials are cleaned before the agent step (clean_git_credentials.sh). So every git operation that modifies the remote must go through safe-outputs' patch mechanism. But git am fundamentally cannot apply merge commits — it only handles linear patches.

This creates an impossible situation for long-running branches:

• The branch falls behind main → needs a merge
• The agent merges main locally → can't push the merge (no credentials)
• The patch includes the merge → git am fails
• The branch stays behind → next iteration hits the same problem
• Evergreen picks it up → same patch failure → infinite retry loop

On githubnext/tsessebe, Evergreen has been failing on this same conflict for days (every run since May 3), burning tokens on every attempt.

Possible fixes

Option A: Let the agent push merges directly

Provide git credentials to the agent (e.g., via GH_AW_CI_TRIGGER_TOKEN) so it can git push merge commits without going through the patch mechanism. The patch mechanism would only be used for create_pull_request (new PRs), not for updating existing branches.

Option B: Handle merge commits in patch generation

Instead of git format-patch (which serializes each commit including merges), generate a single diff patch (git diff origin/branch..branch) that collapses all changes into one patch. This loses individual commit history but avoids the merge commit problem.

Option C: Two-phase push for merges

Split the push into two operations:

1. First push: merge main into the branch (could use the GitHub merge API POST /repos/{owner}/{repo}/merges which doesn't require local credentials)
2. Second push: the agent's actual changes on top of the merged branch (clean incremental patch)

Option D: GitHub API merge

Use the GitHub API to merge the default branch into the PR branch (POST /repos/{owner}/{repo}/merges or PUT /repos/{owner}/{repo}/pulls/{pull_number}/update-branch) during the agent step via the GitHub MCP server. This updates the remote branch without needing local git credentials or the patch mechanism.

Impact

• All three autoloop programs on githubnext/tsessebe are affected whenever their branches fall behind main
• Evergreen is stuck in an infinite retry loop on PR Add claude/code tets for alias triggers #262
• Example failing runs: https://github.com/githubnext/tsessebe/actions/runs/25359092545, https://github.com/githubnext/tsessebe/actions/runs/25298783379

Related

• Evergreen: always merge main first, then fix CI githubnext/tsessebe#266 — Evergreen should merge main first, then fix CI
• create_pull_request patch uses stale origin/branchName instead of merge-base with default branch #28955 — stale patch base ref (fixed in v0.71.2)
• create_pull_request should reuse existing branch when preserve-branch-name is enabled #29152 — recreate-ref for reusing existing branches (fixed in v0.71.2)