General mod fixes, few reverts, and misc changes

Issues fixed: #28 (closed), #49 (closed), #58 (closed), #60 (closed)

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

General mod application via applyMods fixed.
Mod ID issues due to applyMods fixed.
Reverted somnambulist mods and staff of fireballs alter.
Reverted Mod mods setter.
Players can now drown. Yay! (breath fixed).
Stats check for mods in apply().
Some warnings added, some warnings removed.
Tagsets can now remove mods.
Updated Atmod regex.
Permods can now accept decimal per values.
Atmod & Permod 0 values are no longer changed to 1.
Added/updated some comments.