Fix up a number of .gitignore entries.

Most of these were caused by c41b090.
Use the protobuf jar file from the system.

Either sysjarsdir or jars.protobuf can be overridden in local.properties.
Use whatever version of protobuf is on the system.

The protobuf library is fairly stable, what we really want is "the same
version as the protoc binary", and this is the best odds, IMHO.