Fix regular expression matching of old and intermediate adjlists.
Don't default to fromOldAdjacencyList when fromAdjacencyList function fails.

The fromAdjacencyList function may be failing from other issues.  Rely on the
regex to detect old and intermediate style adjlists properly.
Raise InvalidAdjacencyListError if wildcards get assigned in a molecule adjlist.

Wildcards like x should only be used to construct groups.  We construct atoms
for a molecule like so:

atom = Atom(atomType[0], unpairedElectrons[0], partialCharges[0], label, lonePairs[0])

However, we should actually ensure that each list has only a single item and does not
include wildcards.

Also includes a wildcard adjlist unit test to ensure the proper error is raised.
Change CO representation to SMILES='[C-]#[O+]', which is the true ground state.

We probably want resonance to the double bonded state later through charge resonance.
However [C+]#[O-] is completely wrong.
Consistency check for molecule adjlists by checking valency against p,u,c values.

Prior to this, the lone pairs were calculated using the given number of
radical electrons, and the charges were then set automatically with complete
disregard to user-specified charge.  Now, assume u and c to be implicitly zero
unless otherwise specified.  Therefore, if either u or c are nonzero,
they must be explicitly indicated or else they will fail the valency check.

We may want some group checks in the future.

Also includes fixes to unit tests to include these explicit charges and lone pairs.
Make a unit test for an incorrect new-style adjlist.
Remove deprecated checkWellFormed and old databaseTest scripts.
Allow depository reactions to store reactants and products as Species.

This is easier for saving the dictionaries and looking at the reactions.. However
some of the copy functions don't work when the reaction has Species objects so we
need to change some of the code.  (This is probably something we need to fix in the
future so that reactions can be copied when their reactants and products are
Species rather than Molecule objects. But this is a faster fix.)
Clean up Database object's saveDictionary function.
Fix undefined pdepNetworks in RMG simulation under sensitivity.
Fix and update RMG example input files.

Removal of deprecated comments.  Fixes to some adjlists.