Switch a handful of flags over to the new registration style.

This includes a superclass-subclass scenario (ConsoleTask-ListGoals)
and a GroupTask scenario (JvmCompile).

Note that the code that reads and uses the flags needn't change yet.
The legacy flags layer places the values in the existing destinations.

Note: Relies on https://rbcommons.com/s/twitter/r/1096/.

Once this is in I will write up a quick guide to porting flags,
and then we can set ourselves loose on them!

Testing Done:
Ran all tests. Manually ran the relevant pants goals with various flag settings.

Reviewed at https://rbcommons.com/s/twitter/r/1097/
Patch code review comment fixes back in.

They got lost due to my misuse of ./rbt.