I am having issues with excludes for source files not working when using plexus-compiler-eclipse and <compilerId>eclipse</compilerId>. It works just fine when using <compilerId>javac</compilerId>. I have prepared a reproduction test case at https://github.com/wilx/plexus-compiler-eclipse-issue.
This is important to work if I want to compile most of the sources with specific Java target and some with different Java target.