Moved domain.proto to src/main/proto directory
Updated protocol buffer generation support.

* Updated subprojects.gradle to handle changes from main build.gradle file
* Moved sources jar task to afterEvaluate block, it now produces sources from protocol buffer generated projects
Moved sources and jar task to afterEvaluate block
Added generated-* to flag that any generated directory must not be part of a commit.
Formatted code for better readability.