The Modify menu provides different ways for direct modifications of the repository.
You can use Create Directory to create a new directory in the currently selected directory. Enter Directory Name and a Commit Message, which is automatically constructed, as long as you don't modify it manually.
With Remove you can remove the currently selected directory or file from the repository and enter a corresponding Commit Message. Of course, the directory/file is not destroyed, but only removed for the next revision.
Use Copy to create a copy of the selected directory. The directory Copy From will be copied to Destination Path with the attached Commit Message. See also Copy URL-URL.