protobuffers know what files they will generate for zips/jars.

Preliminary support for compressed archives as sources. Currently .zips, .jars, tars, tar.gzs, and tar.bz2s work for protobuffers. Code is fairly extensible, with generic functionality in zipped_sources such that not much code is needed in protobuf_gen (or other targets in the future).
This looks dubious to me.  What are you trying to do here?  Are you trying to eliminate a prefix directory?