This quick tutorial shows how to create an advanced patch that removes and adds files, while doing as much as possible in the Tower UI. The changes are made normally and saved, and then staged as if preparing for a commit. Then the following command is used in Terminal to generate the patch:

git diff --staged > patch-name.patch

or

git diff --cached > patch-name.patch

See kernel.org/pub/software/scm/git/docs/git-diff.html for more details.