Copilot Coding Agent session overwrites custom actions/checkout options silently

[darcien]

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Problems

I have a custom .github/workflows/copilot-setup-steps.yml with actions/checkout@v4 step.
From my understanding, the steps in the copilot-setup-steps should have no restriction.

But from my observation, when Copilot Coding Agent starts a new session, actions/checkout@v4 custom options are being overwritten.

I'll give an example

# .github/workflows/copilot-setup-steps.yml
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
        with:
          # Note how I have custom options here
          fetch-depth: 0
          persist-credentials: true

These options are respected just fine if the workflow runs are triggered not via agent session, e.g. via PR push. Even if the one pushing the PR is the coding agent. I've tested it because I'm making these changes using agent.

This is the log after agent pushed the updates:

After custom workflow has been merged, I created a new issue and assigned copilot to it.

Note how the options for actions/checkout are overwritten in the agent session:

Questions

• Is this an expected behavior?
• If this is expected, shouldn't this be documented? And what about other actions?

Expectations

• Either this should be clearly documented,
• or copilot should yell at me if it's going be to overwritten,
• or this is a bug and should not happen in the first place.

Use case

Specific to my use case, I need other branches to be available locally in the agent session.
The common solution here is use the persisted git credentials from actions/checkout in next step to manually call git fetch. These credentials will be cleaned up in the post job step automatically anyway.

Workaround?

As temporary workaround, I'm using the built in GH token from the action env to authenticate with GH and do fetch.

      - name: Fetch main branch
        run: |
          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}.git
          git fetch origin main:main

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[astafan8]

Any ETA on addressing this issue? It prevents my team to use GitHub Copilot on our repositories. The documentation claims that custom checkout steps are allowed and they will be respected, however in reality that's not the case.

[astafan8]

experiencing the same issue in microsoft/qcodes repo

[stevoland]

@darcien Nice workaround, thanks I will try this.

This decision to not persist git credentials has obviously been made deliberately (for security?) and it would be great for github to at least provide their reasoning and whether this feature loss is likely to be long-term.

The impact is huge. Here's a run from June where the author says @copilot fix these merge conflicts (a common chore that LLMs can very well help with) and they were well obliged

Now the agent can only say something like:

Any remaining merge conflicts with master would need to be resolved at the GitHub level since I don't have direct access to fetch and merge with the master branch.

This is a very poor experience

[stevoland]

As of this week, it seems persist-credentials is no longer overwritten.

However, if the setup checkout persist-credentials: true (default), the agent cannot push (401).

As it seems the agent is operating on a fork, this workaround is allowing me to direct the agent to update the head branch:

# .github/workflows/copilot-setup-steps.yml
  steps:
    - uses: actions/checkout@v4
      with:
        persist-credentials: false

    - name: Get base branch name
      if: ${{ github.event_name == 'dynamic' && inputs.github-token }}
      id: base
      shell: bash
      run: |
        BRANCH=$(echo $COPILOT_AGENT_INPUTS | jq -r '.COPILOT_AGENT_BASE_COMMIT')
        echo "branch=$(echo "$BRANCH" | sed 's#refs/heads/##')" >> "$GITHUB_OUTPUT"
      env:
        COPILOT_AGENT_INPUTS: ${{ github.event.inputs.COPILOT_AGENT_INPUTS }}

    - name: Fetch base branch (workaround allowing agent to update with base)
      if: ${{ github.event_name == 'dynamic' && inputs.github-token }}
      shell: bash
      run: |
        git remote add upstream https://x-access-token:$TOKEN@github.com/$GITHUB_REPOSITORY.git
        git fetch upstream $BASE
      env:
        BASE: ${{ steps.base.branch }}
        TOKEN: ${{ secrets.GITHUB_TOKEN }}

So prompts like "@copilot merge in upstream branch, fix conflicts, pick mine" seems to work

[pheu]

I was struck by the same thing recently. I need fetch-depth: 0 to be respected, but it's silently being changed to fetch-depth: 2 whenever Copilot work.

[AdamVig]

This behavior is documented, for what it's worth:

Any value that is set for the fetch-depth option of the actions/checkout action will be overridden to allow the agent to rollback commits upon request, while mitigating security risks.

I'm finding that Copilot Coding Agent can't run git push to my private repository, and I wonder if it's caused by Copilot overriding the default actions/checkout persist-credentials: true:

- name: Checkout repository
  uses: actions/checkout@v5
  # Copilot sets its own `fetch-depth` setting, no point in setting it here as it would be overridden

Run actions/checkout@v5
  with:
    fetch-depth: 2
    persist-credentials: false

I had it run git config --list and didn't find anything interesting in it, but thought I'd share it here in case it helps anyone:

safe.directory=*
filter.lfs.clean=git-lfs clean -- %f
filter.lfs.smudge=git-lfs smudge -- %f
filter.lfs.process=git-lfs filter-process
filter.lfs.required=true
core.repositoryformatversion=0
core.filemode=true
core.bare=false
core.logallrefupdates=true
remote.origin.url=https://github.com/<my private repository>
remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*
gc.auto=0
branch.copilot/<the branch>.remote=origin
branch.copilot/<the branch>.merge=refs/heads/copilot/<the branch>
credential.username=copilot-swe-agent[bot]
credential.helper=!f() { test "$1" = get && echo "******"; }; f
user.email=<random 9-digit number>+Copilot@users.noreply.github.com
user.name=copilot-swe-agent[bot]
pull.rebase=false

Update: even when I explicitly set persist-credentials: true, it is overwritten:

Run actions/checkout@v5
  with:
    fetch-depth: 2
    persist-credentials: false

As a result, Copilot coding agent is unable to push its changes in my main monorepo!

[darcien]

Thanks for the docs link, seems like it wasn't there when I raised this question (that doco for fetch-depth was added on August 2025 github/docs@08f1bd2).

I wish GitHub could add doco for other options too, not just fetch-depth.