Ok I am so close to reproducing a consistent setup I could scream. the first and MOST IMPORTANT hint I'm gonna give everyone is, when you setup your directories, like the source dir, resources, libs etc... SET THE OUTPUT PATH TO THE DIRECTORY ITSELF! Don't ask me why, I think that's terrible, perhaps it's a side effect of the code changing.
Yes what I mean is that if you have
resouces (xml files for struts etc..)
The output path for src is the src dir
The output path for resouces is the resouces dir
what will happen if you do this is that they will both end up in the WEB-INF/classes directory like they should be, or if you want resouces under WEB-INF simply edit the J2EE deployment screen and point them there. If you don't point the output directory to itself, it will not work right, you'll get all sorts of cannot copy errors because it would make things recursive, or the directories will end up in 2 places, or not be copied at all.
This is nuts, but I have a webapp working!