Support custom root dir for Protobuf local references

[ImFlog]

Following #166 and quoting @Jtalk :

I've added an example, but it won't compile due to how Wire is configured right now: it links the whole Protobuf model, meaning it's not going to work with 2 files providing the same message (Company) sitting within the same Protobuf root. It's possible to either skip linking & doing import lookup ourselves, based on the root dir, or to make the root dir configurable (something I wanted to ask for separately, as our schema files live outside the Gradle project the plugin is in).

This should allow this commit to work as expected (it's failing for now).