The use of Subversion with Eclipse is producing major problems.
Today I found out tha by default, Eclipse Java Builder copies all the non-java files under the source folder into the build output folder. This causes a problem if you are using Subversion, which creates a .svn folder under every workset folder.
So the solution ito prevent Eclipse from copying the .svn folders, is to go to Preferences->Java->Compiler->Building, expand the “Output folder”, and add “.svn” to “Filtered Resources”.
http://www.digizenstudio.com/blog/2005/05/07/prevent-eclipse-from-copying-svn-folders/