The project requires that all JavaDoc for public methods exist and are valid (e.g., have all @param, @return and @throws to match the signature). However, the generated Java source for Protobuf contain numerous JavaDoc errors relative to these settings. This causes lots of errors inside Eclipse (and probably other IDEs), but ignoring/disabling the JavaDoc errors leads to improper JavaDoc (fixed in next commit). By moving the generated Protobuf source code to a separate directory (e.g., src/gen/java), the IDEs can ignore any compiler and JavaDoc errors/warnings for those files, while keeping the more strict JavaDoc checking enabled for the rest of the code.