Fix to docker import issues and swagger error

This is actually two fixes in one change:
1. Fixing the import issues in the docker containers, also cleaning
   it up.
2. Avoiding the creation of multiple swagger.json files by specifying
   which of the proto files represent the top-level service.

Change-Id: I9fec5cf48df127725673ba53f0e91d2ed2e275ad
3 files changed