Sparse-checkout configuration persists across workflows on self-hosted runners

[Bug] Sparse-checkout settings from actions/checkout persist and affect subsequent workflows on self-hosted runners

Summary

When using actions/checkout with sparse-checkout on a self-hosted runner, the sparse-checkout Git configuration persists across subsequent jobs. This causes later workflows (that do not use sparse-checkout) to only check out the previously sparse file set instead of the full repository.

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Prerequisite

• A self-hosted GitHub Actions runner is configured and available.

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Steps to Reproduce

1. Run a workflow with sparse-checkout

   - name: Checkout specific file from sample-repo
     uses: actions/checkout@v4
     with:
       lfs: true
       repository: org-name/sample-repo
       token: ${{ secrets.SAMPLE_TOKEN }} # Contains a PAT
       path: sample-repo
       sparse-checkout: |
         sample-file.bak
       sparse-checkout-cone-mode: false
       clean: false
   

   Allow the workflow to complete.

2. Run a second workflow on the same self-hosted runner (no sparse-checkout):

   - uses: actions/checkout@v4
     with:
       clean: true
   

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Expected Behavior

The second workflow should check out the entire repository, unaffected by the sparse-checkout configuration from the previous workflow.

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Actual Behavior

• The second workflow:
  • Removes all files.
  • Only checks out the files that were previously specified in the sparse-checkout configuration from the first workflow.
• This indicates that core.sparseCheckout remains set to true in the runner’s Git configuration between jobs.

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Analysis

• The actions/checkout action modifies the runner’s Git config:

  git config core.sparseCheckout true
  

• On self-hosted runners, this configuration persists across jobs and workflows.
• Unless explicitly reset, future runs on that runner inherit the sparse-checkout state.

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Temporary Workaround

Manually disable sparse-checkout after using it:

- name: Disable sparse checkout
  run: git config core.sparseCheckout false
  continue-on-error: true

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Proposed Fix

Ensure actions/checkout:

1. Resets core.sparseCheckout to false at the start of each execution.
2. Does not persist sparse-checkout state between runs on the same runner.

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Reproducibility

• 100% reproducible.
• Can be tested without relying on our workflow execution references.

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Environment

• actions/checkout: v4
• Runner type: Self-hosted
• OS: Windows

No source file or test is named. Start by tracing actions/checkout's sparse-checkout configuration handling and reproduce the two-workflow sequence on a self-hosted Windows runner. Done means a later checkout without sparse-checkout restores the full repository instead of inheriting the earlier sparse file set.