The manual is a work in progress. Please add to it with complete, tested instructions wherever you can.
To uninstall Huggle, follow these instructions. If you want to remove all of your configuration options, blank Special:Mypage/huggle3.css or Special:Mypage/huggle.css
There should be a shortcut to "uninstall Huggle", using that will uninstall Huggle. On Windows, there may be some leftovers in your Program Files (under the folder Huggle) which can also be deleted. Your personal configuration is in AppData/Local/Wikimedia/Huggle and can be also deleted if you want.
Just delete Huggle from your Applications folder. You may also delete your personal configuration that can be found in ~/Library/Application Support/Wikimedia/Huggle.
Debian / Ubuntu
You can safely remove Huggle using Package Manager.
When you ran the "make install", a file called install_manifest was generated in current folder. It contains the location of all files there were installed. By removing these files, you will uninstall Huggle. See FAQ for more information.