Fixes duplicate class errors

Fixed the "already added" bug by simply ignoring duplicate classes that are added. This may not be a "perfect" solution, but it's massively better than the current state, which is "it won't build at all". This is in line with how java works in general anyways, so it shouldn't be a huge surprise if someone comes across this behavior accidentally. Since this bug has been in the tools for 3 revisions, it's due to be fixed now, one way or another.

This addresses bugs 228 (4 stars), 20398 (36 stars), 20956 (48 stars).