Examine dependency info for protobuf and scrooge

For unclear reasons, protobuf and scrooge support only direct and transitive dependency modes, and do not support unused deps. We should figure out what better makes sense here.

Relates to comments on https://github.com/bazelbuild/rules_scala/pull/975

Start by reading the comments linked from rules_scala pull request 975, then compare the current direct and transitive dependency modes for protobuf and scrooge. Define which dependency behavior should be supported and how it differs from unused dependencies; the issue is done when that behavior is agreed and can be specified for implementation.

Written by the indexing model from the issue text.