A couple days ago I decided it was time to upgrade Eclipse from 3.5 to 3.6.
My 3.5 version was installed from the Zend Debugger+PDT all-in-one initially. Because I didn't feel like rebuilding my custom perspective I figured just adding the 3.6 update site and upgrading would be the easiest route.
The upgrade went fine and all my settings seem to have been preserved, but code assist is not working for any of my existing projects and I cannot Cmd+click on a class name to open the file containing that class for editing.
I've tried cleaning the project and rebuilding it and I have verified that the buildpath configuration didn't get nuked. What am I missing?
So it seems that upgrading was actually a bad idea. Some sort of incompatibility seemed to be the issue. I did an intstall with the new all-in-one (64 bit) and everything works as it should.