The requested functionality is currently possible using normal mercurial features ( clone -> make changes to the cloned repo -> commit changes to the cloned repo -> push changes to the tool shed repo ).

It is also currently possible to upload a new tarball to any "upload point" (position) in the tool shed repository by selecting the upload point in the built-in repository file browser. - The hierarchy that the uploaded tarball contains will be added to that upload point in the tool shed repository. - Any files in the uploaded tarball that do not currently exist in the tool shed repository will be added. - Any files that exist in the hierarchy of the uploaded tarball that also exist in the same location of the hierarchy of the repository relative to the upload point will be replaced in the repository.

It is on my list to: Delete any files that do not exist in the uploaded tarball's hierarchy but that do existin the same position of the tool shed repository's hierarchy relative to the upload point. This feature will require clear documented communication to the user, which I've not yet had a chance to do, but will soon.

You can currently delete specific files by cloning the repository, making any changes you want (including deleting), and committing and pushing the changes using mercurial's command line.

I've added it to my list to provide a feature allowing a user to select a specific file in the repository (hopefully using the built-in file browser) and deleting the file in some way that doesn't require mercurial's command line, but in the meantime, use the above existing feature.