Upgrade protobuf library to 3.0

protobuf no longer uses the FFI interface so this requires shelling out.
This currently a very naive implementation using popen which wraps the
command in sh -c to capture stdout. which is obviously going to break on
every platform that doesn't have sh.
Bump version to 0.6.4
Update todo list.
Fix requeuing.

The requeue method was trying to instantiate a new ACL based on the
hashed ACL not the the actual ACL. All of which is by the by as it
already has fully formed ACL that it can use directly!
Minor changes to log messages.
Check to see if the agency is running earlier.

This checks so see if the agency is running in the constructor and
raises an exception it is.
Bump version to 0.6.5.