Add warning for files include by vendor path that should be from GOPATH

[stevvooe]

There are cases where the same file can be included relative to vendor or GOPATH. In GOPATH, they might look like this:

github.com/myproject/foo/vendor/github.com/otherproject/foo/foo.proto

As referenced through vendor, they would look as follows:

github.com/otherproject/foo/foo.proto

We should detect these cases and warn the user to use the shorter, vendored version.