Fixed problems with creating species through API.

The parser was still making calls to the API's helper functions instead
of using the API calls directly. This has been mostly fixed. The one
area that still needs updated is the printing of species information
(e.g. printing out l_r_bar).

Instead of passing a large number of parameters to mcell_create_species,
it now just takes a pointer to a mcell_species struct. This prevents
"Parameter Hell" and should prevent breaking the API with future
changes.

Some now extraneous functions were also removed.
Fixed how the printing of species info is handled.

The final step of parsing molecules/species definitions is printing
summary information about them. This was directly interacting with the
internal "world" simulation state instead of using information received
via the API. This has been resolved.

Unfortunately, this meant re-incorporating sections of code which were
removed during the last commit. It might be worthwhile investigating
this in the future to see if some of the redundant sections can be
removed.