Cleaned up species creation code.

-Renamed filename to be consistent with planned changes
 (e.g. create_reaction.c, create_geometry.c, etc).
-Renamed several functions and variables for the sake of clarity.
-Added header guard to create_species.h.
-Removed unneeded function from create_species.
-Removed inclusion of mdlparse_aux.h from create_species.c/h to keep
 parser and API decoupled
-Removed print statements from API (The API should be mostly "quiet."
 Either success or failure (with a possible error code)).
-Cleaned up formatting (indenting, etc).
Fixed formatting (function comments, indenting)