Use a single proto file for C and Java

The contents of https://github.com/square/subzero/tree/master/core/proto/squareup/subzero and https://github.com/square/subzero/tree/master/java/proto/src/main/proto/squareup/subzero can probably be merged. Perhaps under common/proto/squareup/subzero?

Historically, we had these different directories because the code lived in different repos.