Every once in a while, when I do a design refresh for one of my XPages databases, I notice it adding .class files for XPages that I’ve already deleted. 
So, I do another clean & build on the template, but they’re still there. Annoyed, I console myself that the files are never referenced, so I don’t need to worry about it. Of course, I worry anyway.
So, in my quest to figure out what was going on, I continued poking around. I checked in the Local folder while looking at the Navigator Eclipse view and saw that the .java files were still sitting there as orphans, with no XPage in the design any more. So, I did just a ‘Clean’ and it eliminated all the files except for those. According to “Mastering XPages”, this doesn’t happen. In warning you not to create Java files in the Local folder, it states that
the incremental builder in Domino Designer would then flush the contents of the Local folder before recompiling all the XPages again. Your custom Java source files would be permanently deleted in this case.
Yet, those files stubbornly remain. Fortunately, when I create a new copy of the template, none of those Local files copy into the new database. So, my habit of creating new files for new versions of the template has helped me by dodging this little, harmless bug.
Lost in Code 