Damn, I should have thought to suggest that. That will be fixed in the next version and you'll only have to click once.
Congratulations on getting everything working.
If you (or jose or anyone else) would like, we'd love to have a howto for getting Arduino running under linux. We have some preliminary instructions in the general build instructions:
http://svn.berlios.de/viewcvs/arduino/trunk/build/howto.txt?view=markup
and a few notes in the comments at the top of the linux make.sh: