To take a folder and start tracking its changes, just right-click it and then
Git -> Create new.
Hint 1: You can't put a git repository inside another repository. If you don't see
Create new as an option, you're probably inside an existing repository, and you need to move up to a higher folder.
Hint 2: Rather than using the text bar at the top of the window, you can use any of the methods described in the DiffPlug quickstart to get the context-menu for a file.
Now that you've got an empty repository, you can start making commits.