Minor Description
For resource files that are closely related to a .java file, I often skip src/main/resources and put the file into src/main/java next to its corresponding .java file.
This requires an easy but fairly boilerplate line of:
project.resources.from(_('src/main/java')).exclude('*.java')
In my buildfile. Besides reducing boilerplate, I always forget to add this, so I've got caught by it several times.
It seems like this would be a reasonable default because, .svn/etc. folders aside, I would think non-java src/main/java files showing up in the jar/war would be expected and desirable more often than not.