Generate *all* protos in the script, applying fixups.

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.