You can delete an individual file in your repository.
If you try to delete a file in a repository that you don’t have write permissions to, we'll fork the project to your user account and help you send a pull request to the original repository after you commit your change. For more information, see "About pull requests."
If the file you deleted contains sensitive data, the data will still be available in the repository's Git history. To completely remove the file from GitHub Enterprise Server, you must remove the file from your repository's history. For more information, see "Removing sensitive data from a repository."