Removed unused parameters.
Bugfix: Initializing symbol table for counting

This fixes a problem that was introduced in a recent refactoring.  With
that said, it's not really clear what the the point of the
counter_by_name symbol table is. Aside from the functions touched in
this commit, it's only used by a function that isn't called during a
normal simulation (get_counter_trigger_column). As such, the bug didn't
cause any serious breakage.
Fix small memory leak related to object transforms

The vectors associated with SCALE, ROTATE, and TRANSLATE weren't being
freed.
Fix memory leak related to species definitions.

Removed some redundant mallocs, since species were already being mallocd
in store_sym.