Md5.dat on website needs update! Fix startup for real.

The md5.dat at http://files.mcupdater.com/md5.dat needs to be updated.
It is out-of-date and is also formatted incorrectly for how the program
parses it.  The version in this commit is formatted and up-to-date at
the time of posting.
Starting to convert folder hierarchy to be similar to current
.minecraft.  Allows for libraries to be used by multiple instances if
they share that same dependency,
Moved some code around, Added comments to start figuring out what is
going on in places, formatting.