Chunky Mod Fixes.

Issues fixed: #49 (closed), #58 (closed), #60 (closed), #62 (closed)

Partial fix: #54 (closed) (second half)

Edits: #28 (closed), #48 (closed), #55 (closed)

General mod application via applyMods fixed.
Mod ID issues due to applyMods fixed.
Allowing slightly more complex mods.
Reverts and fixes in the JSON data files.
Stats check for mods in apply (the sublimate fix edit).
Tagsets can now remove mods.
Mods regex updated so that percent mods don't get improperly processed.
Updated Atmod and Permod regex so that they don't accept odd inputs and break.
Permods can now accept decimal per values.
percent mods now properly transfer to another mod.
Atmod & Permod 0 values are no longer changed to 1.
Some warnings added, some warnings removed.
Added/updated some comments.

There's probably things I forgot to mention here.