Update protobuf to 2.5.0.

And use the maven plugin, which additionally takes care of detecting incompatibilities between the protobuf-java and protoc.

Instead of fighting constant battles over which version is in the path and what comes with the operating system,  assume source checkout relative to build area and compile there (but not necessarily install). The files we need are protoc (which would be in /usr[/local]/bin) and google/protobuf/descriptor.proto (which would be in /usr[/local]/include).

I am open to suggestions on other ways to accomplish this. If this one is okay, I will take care of updating the build machines before we kick this off.