Repository Cleanup, Mod Compat

Made a few misc changes for the heck of it.

-Fixed crash with mod instance
-Updated README
-Added api folder with dependencies used by AA.
-Made spawn rarity of entities configurable
  -nerfed eagle spawns while I was at it.  I may make max and min of spawn groups configurable too.
-thaumcraft compat


I should note that I have changed the run directory where minecraft throws its files to comply with gradle updates.  The folder where game files are thrown inside is now called 'minecraft_client' rather than 'eclipse'.

Also, regarding thaumcraft, I don't know how you want to balance aspects, soooo.... yeah, I will wait for an opinion.