Protobuf and payload cleanups

Moved some of the protobuf examples around to be more consistent.
Some cleanups from payload refactoring
Added a deprecation message for the unused 'buildflags' attribute in java_protobuf_library
Removed the ability to use a jar_dependency in java_protobuf_library imports.

Testing Done:
CI is green.
Added a unit test for the java_protobuf_library target

Bugs closed: 623

Reviewed at https://rbcommons.com/s/twitter/r/1099/
Sync of https://github.com/pantsbuild/pants/commit/0ea28ad0dfa94411a51d8c666aa780d3f254d786