Organization changes

--Changed to new file directory on main computer, so dependency paths
are updated
--Simplified package structure
--Added additional methods that will distribute data based on the
command, greatly simplifying Main.onCommand() to only a few lines.
--Added Commands.getProperties(String command) that returns a
CommandProperties object
--Added doCommand() to PlayerCommands and ConsoleCommands, that will act
as shells for the command methods
--Made CommandInstance.setTarget return the target (potentially null)
which makes the client a little simpler
--Wherever possible, changed player strings to player uuid, which
removes a lot of deprecated warnings.
--Updated version number from 2.2.0 to 2.2.1
Fixed null target bug

An error in CommandInstance could lead to the target being null, but the
report saying that the target was not null, leading to countless null
pointer exceptions. Now, CommandInstance will handle all target setting,
and will not set the flag to true if the target is null.
Simplified Main.prepare()

Basically pushed functionality into different methods in CommandInstance
Fix a bug in plugin.yml

Changed main package and increased version. The plugin is also now
stable and ready to be merged to master.