ProtoParser is a simple Java project that parses .proto files. It’s a dumb parser: whenever you reference a type, it lacks any mechanism to resolve that reference.
Wire is a much more sophisticated Java project that builds upon ProtoParser. It performs that essential linking to make ProtoParser’s output useful, and then uses that message graph to generate nice model classes.
I’m in the process of folding ProtoParser into Wire, combining the two projects into one. The result will be a new subproject (called wire-schema) that does both parsing and linking. This is how we should have done it all along. That new API isn't stable yet, but it will be soon.
If you’re using ProtoParser, be warned: we’re halting development on that project. That’ll allow us to move faster on Wire, which will has a better, more powerful schema model.