Added groups remove command

Also patched an issue with writing XML files that can cause syntax corruption
when removing the last element of a file
Refactored CommandSystem Step 1

Changed from per-class commands to per-method commands,
quite like PluginListener works.
Integrated registering Help into the registration of commands itself.
So only one call is needed.

A couple of minor fixes I amde during redoing the commands

Permission node changes