So if the failed setup.command is to blame, how would one go about removing (or undoing) the setup
There's no real need to undo the setup, as it's just creating a single directory that other traditional unix applications (e.g. kermit, IIRC) may conceivably use. If you're trying to "remove and reinstall", don't bother - just run the stup again.
That didn't work, I've tried that a few times already, and restart and shut down after 2 or 3 of the attempts.
Like most OS X apps, just delete the application from /Applications and that's good enough.
-j
That's not really true either, there are at least pref files in ~/Library/Arduino... I was asking if there are any more things like that which may be responsible for the conflict. For instance, version 0006 required me changing the min version of Java, to 1.5 from 1.4 (in the info.plist inside the app bundle) in order for it to run.