Change tree in statmech groups

The previous tree did not reflect the previous definitions at all. I have
made (quite sweeping) changes to the tree to make it fit the group
definitions.

In addition I have modified some definitions for consistency:
-Add "Ketone" to "RdCsR2" ORgroup definition
-Add "Nitrites" "Nitroso" ORgroup definition
-Add "Nitrates" "Nitro" ORgroup definition

This last part has almost certinaly made some groups with overlapping
definitions. This will be fixed in later commits, presumably with the aid
of the appropraite unit tests.
Overhaul statmech groups to include X wildcard radicals

The previous groups in statmech were created before we allowed wildcards
for radicals. As a result there were a lot of subgroups that are now
unnecessary. I have mostly deleted these groups.

Also there were a couple changes to group definitions. From the original
source of Goldsmith's thesis, it became obvious that some of the R!H atoms
types should actually be C:

-changed RdCsR2 into CdCsR2
-Moved ketone up one level from L5 to L4 was under RdCsR2
-changed RsCsR3 to CsCsC3- the way Frankling wrote the frequncies and the
symmetry number suggests it was only intended for carbons
-Changed a R!H in ketene to a C, to match the definition of ketene
-Changed name ROOH to COOH, which matches the definition
-Changed name ROOR to COOC, which matches the definition

The following groups are unclear, but I also think they should be all C:
-RsCHsR2
-CtCsR

However, I did not change anything for those two groups
Changed {2T,2S} to 2T in groups.py of statmech

Having the {2T,2S} is incompatabile for the new AdjList change. For all
these cases I changed it to 2T, as this is likely to be the ground state.

changed the following to 2T only
-"R!Hx2"
-"C_R2"
-"RsCHrr"
-"RdCrr"
-"RsCrrsR"
-"Ether"

changed "R!Hx3" to 3D only
Add lone pair denomination for R!Hx3 group in statmech to make groups R!Hx2 and R!Hx3 non-identical.

RMG-Py was detecting R!Hx1 and R1Hx3 to be equal:

R!Hx1
1 * R!H 1

R!Hx3
1 * R!H 3D

This was because 3D actually implies a single unpaired electron and 1 lone pair.
However, when the group does not have a lone pair denomination, it allows any
number of lone pairs, therefore making these two groups identical.

This is a mostly temporary fix.  These two groups are clearly overlapping when
R!Hx1 can allow any number of lone pairs including 1 lone pair.
Remove cis thermo groups that cannot be found by RMG.

Cis groups with double-labeled atoms cannot ever be incorporated into RMG's thermo
since there is no cis or trans distinction.  It makes more sense to delete them
unless we have that functionality (based on Bill's recommendation) and also
to make the database unit tests work for these.
Fix 1-hydroxybutyl + O2 training reaction in R_Recombination which had unsaturated adjlists.
Add missing label to reactant in training rxn in R_Recombination family.
In statmech, remove single group LogicOr groups and replace them with the adjlists directly.
Consolidate identical species in Dooley/methylformate kinetics library.

Changed species HO2CH2OCHO to HO2CH2OCHO.
Changed species C3KET21 to CH3COCH2O2H.
Consolidate identical species in GRI-Mech3.0-N.

Change species O to O(T).
Fix Nitro group to be a parent of Nitrates group in statmech groups.
Removed Cb atomtype from Cds-noH in abraham solvation group so that it is proper child of Cds.
Fixes to thermo radical groups so that they obey parent-child relationships.

Most changes were related to parents being Cs or Cd atomtypes but children
being more broad C atomtype.

2 real fixes:
-CO was previously not found to be a child of Radical parent.  Now it is
assigned as a child of RJ2_singlet.
-CdJ2-Sd_singlet was incorrectly assigned as L5 group rather than L4.
Fixes to thermo groups 'group' so that parent-child relationships are correct.

Most fixes were related to parents being more specific than children, so
many C's were converted to CO's or CS's but were accurate groups and
correct parent-child relationships.

Major fix:
-Changing CsJ to include CS atomtypes as well as Cd and CO to now include the
C=S related groups underneath it in the tree.

Additional fixes include:

-Assigning Cs-NNCsH to Cs-NNCsCs which was what it actually described.
 Renaming Cs-N5dN5dCsH to Cs-N5dN5dCsCs and putting it under Cs-NNCsCs
-Creating a new Cs-NNCsH group and putting Cs-(N5dOdOs)(N5dOdOs)CsH under it.
-Changing Cb-CbCbN3s from the old adjlist:

1 * Cb  0 {2,B} {3,B} {4,S}
2   Cb  0 {1,B}
3   Cb  0 {1,B}
4   N3s 0 {1,S}

to the new adjlist so that it would be a proper child of Cb-Cb:

1 * Cb  0 {2,S} {3,D} {4,S}
2   Cb  0 {1,S}
3   Cb  0 {1,D}
4   N3s 0 {1,S}

Hopefully this is what Beat intended.
Fixes to thermo ring groups so that parent-child relationships are correct.

Most fixes are making children's atomtypes more specific, i.e. switching O to Os
where appropriate.

Made sixnosidedouble group more broad and inclusive of nitrogen so that Piperidine
can be a child of it.
Fixes to solvation group tree for some nitrogen and sulfur groups.

Fixed up some groups, and the tree, for some parent/child mismatches.