ISPN-4357 Use a specific cache for managing protofiles

Also upgrade to protobuf-2.6.0 and protostream-2.0.0.Alpha3

Jira: https://issues.jboss.org/browse/ISPN-4357
        https://issues.jboss.org/browse/ISPN-4756
I was more interested because it seems only the resolve status is only referenced in the Remove command.  The others only seem to update the keys they affected not all descriptors like Remove.