Conflict in filename of submodules

[zhouyan]

Consider two Protobuf package,

Package 1 has file, /pkg_root_dir/pkg1/core.proto and package 2 has file /pkg_root/pkg2/core.proto, which is not a situation that one be sure that does not exists when working with beyond just one proto package. Now say there's a proto file that either directly or indirectly contains both import pkg1.core and pkg2.core, which are the packages in the two corresponding protobuf files, julia's generator will emit error that try to write core_pb.jltwice. For other languages, the behavior is usually writepkg1/core_pb.cpp pkg2/core_pb.cpp, etc., (possibly different root common directory depending on what is passed to -I`.).

In addition, other languages does not generate implementation/header files for dependencies. Only strictly for proto files that the user requested the generate. This may at first seen inconvenient, but it is a much more scalable process. It gives user much more flexibility in dependency management. That is, it follows the "you get what you ask for" principle, no more no less.