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How to repair a corrupted Index

Background

The Index file (.git/index) is a binary file that contains meta-information about the working tree, including staged changes and file modifications. This file can become corrupted due to various reasons such as system crashes, power failures, disk errors, or hardware failures during Git operations.

If you suspect a corrupted Index, try running git status in your repository. When the Index is corrupted, Git will fail to execute most commands and display error messages like:

$ git status
error: bad index
fatal: index file corrupt

or

$ git status
error: bad signature 0x00000000
fatal: index file corrupt

or

$ git status
error: index uses  extension, which we do not understand
fatal: index file corrupt

When SmartGit encounters a corrupted Index, it will be unable to open or interact with the repository until the issue is resolved.

Note

This kind of problem typically occurs after unexpected system shutdown, disk failure, or when antivirus software interferes with Git operations.

Resolution

The resolution is performed using Git from the command line:

  • cd to your repository.
  • Invoke git status to verify the corruption (you should see the error message).
  • Create a backup of the corrupted .git/index file.
  • Optional but recommended: Create a backup of your entire repository by copying the repository directory to a safe location. This allows potential recovery if needed.
  • Remove the corrupted Index file:
    • On Linux/macOS: rm .git/index
    • On Windows (Command Prompt): del .git\index
    • On Windows (PowerShell): Remove-Item .git\index
  • Rebuild the Index from the last commit by invoking: 
    git reset --mixed

    This command repopulates the Index by reading the tree from HEAD without modifying your working directory files.

Warning

All staged changes will be lost during this process. Any uncommitted changes in your working directory will be preserved, but they will no longer be staged.

  • Verify the Index is repaired by invoking git status again. You should now see a clean status or your unstaged modifications.
  • Now SmartGit should be able to open the repository normally.

Additional Troubleshooting

If the problem persists after rebuilding the Index, consider these additional steps:

  • Check for nested repositories: Sometimes a .git directory exists underneath subdirectories, which can cause issues. Search for any nested .git directories that shouldn’t be there. Before removing them, create a backup by copying them to a safe location, then remove the nested .git directories.
  • Verify repository integrity: Invoke git fsck to perform a file system check. This scans your repository for corruption in commits, tree objects, and other Git structures.
  • Check disk health: Run disk diagnostics to ensure there are no underlying hardware issues causing repeated corruption.