Current task list (not in order)

1) Fix GeneratedBuilder.MergeFrom
2) Extra unit tests for pending Java optimisation
3) Refactor IsInitialized
4) Performance framework
5) Optionally remove dependencies to core and csharp options
6) Remove multifile support
7) Remove bootstrapping hack
8) Improve "regenerating descriptor.proto" hack
10) Mono support
11) Docs
12) Clean up protogen code
13) Add flags to protogen