How to Delete Files and Folders on GitHub
The web interface on GitHub.com allows you to do basic editing tasks. You can delete a specific file after opening its detail view and then clicking on the little trash can icon:

However, you cannot delete multiple files in one go nor can you delete folders in the GitHub web interface.
These tasks must be performed in a local repository, after cloning it to your computer. For an in-depth tutorial on how to clone and work with a local repository, take a look at our free online book on learning Git.
How to Delete Files and Folders in a Local Git Repository
If you're using Git in a desktop GUI like the Tower Git client, you can simply select one or more items - both files and folders - and delete them:
In case you're using Git on the command line, you can use the following commands:
# To delete a file:
$ git rm my-file.txt
# To delete a folder, add the '-r' option:
$ git rm -r my-folder
After deleting the file or folder, don't forget to commit the deletion to record it in the repository.
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