We still have some protos which aren't generated how we want them to be:

- Until we have an option to specify the "umbrella" class, DescriptorProtoFile
  will be broken. (The change of name here affects the reflection descriptor,
  which accounts for most of the change. That's easier than trying to work out
  exactly which occurrences of Descriptor need changing though.)
- That change affects UnittestCustomOptions
- Issue #307 breaks Unittest.cs

After this commit, we don't have the record of the fixups in the files themselves
any more, but one centralized record in the shell script.

(Having regenerated descriptor.proto relative to src, the earlier commented-out code checking that dependencies match may now be okay to uncomment again. Will experiment in later CLs.)

This commit includes changes to the C#-specific protos, and rebuilt versions of the "stock" protos.
The stock protos have been locally updated to have a specific C# namespace, but this is expected to change soon, so hasn't been committed.
Four areas are currently not tested:
1) Serialization - we may restore this at some point, possibly optionally.
2) Services - currently nothing is generated for this; will need to see how it interacts with GRPC
3) Fields beginning with _{digit} - see https://github.com/google/protobuf/issues/308
4) Fields with names which conflict with the declaring type in nasty ways - see https://github.com/google/protobuf/issues/309