You mentioned that it complains about duplicate classes. Can you provide more info? Have you tried finding the classes? What are their names and packages, and where are they precisely
w.r.t to your project structure? If you have the name of a class you can try to find (copies of) it by using the "open type" function (press CTRL-SHIFT-T).
One possible explanation is that there may in fact be duplicate classes that exist in different source folders. If so, that is a known problem in Eclipse/STS.
Eclipse doesn't allow duplicate classes because it compiles all source folders in a project together. With commandline tools (grails in specific) they compile
the source folders separately and so don't experience this limitation. Not sure this is the problem, but it is a possibility.
You seem to be having a lot of problems with Spring Security ACL plugin in STS (I recall a prior issue which is logged here: https://issuetracker.springsource.com/browse/STS-1792).
Could be there is something unusual about the plugin that triggers some bugs in STS.
I'll play around with it a bit myself and see if I can reproduce some of these problems. Keep an eye on the STS-1792 issue, I'll follow up there if I find something.
Kris De Volder -- SpringSource