There is no need to modify anything in IDE 1.0. Just
- connect your AVRISP mkII six-pin header to Uno,
- set Tools - Board - Uno,
- set Tools - Programmer - AVRISP mkII,
- make sure Uno has power.
You must upload using File - Upload using programmer instead of File - Upload.
Just read in the help files that <shift>while clicking upload will upload using the programmer. Looked a long time in the forums to figure out how to upload using my avrispmkii.
To communicate with the USB on Ubuntu I need to run arduino from the terminal using sudo. I don't care if there is a an easier way by changing the rules, every attempt I made doing that failed, it is easier to just run as sudo.