Bugfixes to new Adjacency List

Don't merge yet.  This is a plethora of unit tests and fixes to the adjacency list functions.  I am
leaving these changes on the master new-style-adjacency-list branch so anyone can add on
or modify these commits.

Some issues that still remain:
- CO in the ground state [C-]#[O+] should probably have a resonance form with the double
bonded state C=O which works better with the existing reaction families.
- CH2 (2S) and (2T) still both get translated to 1 C u2 p0 c0 without distinction between the two.  
We will definitely need a separate reaction family for the 2S form....
- We probably need resonance for charged species (lots of nitrogen species would have this)