Since i've not found a thread about tips on this IDE, i'll open this one.
I come from eclipse, i can't request all eclipse features, but at least i can ask some.

1) right click -> delete file on a file project, so that i can delete also the file (and not only removing from the project)

2) Refactor - i live with it! I mean rename a var wherever it appears in your project code.

Post your request here:

http://code.google.com/p/agk/issues/list

This list will be seen by the AppGameKit programmers. Just make a enhancement request there.