Add Cdd atom type to *3 in Intra_R_Add_Exocyclic reaction family.

This is a combination of several commits:

 * Add Cdd atom type to *3 in Intra-R-Add-Enxocyclic reaction family.
 * Added some comments to the longDesc fields.
 * Remove .DS_Store that shouldn't be there
 * Fix minor syntax problems caused by space, also group definitions are case sensitive(Cdd)!
 * Fix typo in Intra_R_Add_Exocyclic

Authors:   Fariba Seyedzadeh Khanshan <seyedzadehkhanshan.f@husky.neu.edu>
           Richard West <r.west@neu.edu>
Allow *3 to be Cdd in the DoubleBond group as well in Intra_R_Add_Exocyclic

The top level groups all allow Cdd atom type as *3, but we would not
descend the tree to get any decent data, because the double bond group was
defined as Cd only. Now at least we will get to a level two node, although
we have no relevant data below this.
Strip whitespace at end of lines
Bugfix for importing and adding history to kinetics families.

Rate rules come in lists because more than one rule may be present per node.
Updates to families from RMG-Java since previous import (Nov 12 2012)

This was done by an automatic import by Connie <connieg@mit.edu>, followed by these corrections:

1) Reverting H-abstraction family back to previous commit
Import script is not able to incorporate many of the manual changes made
to the family.

2) Fixed incorrect import of kinetics in HO2_elimination_from_peroxyradical family

3) Incorrect definition for group "OJ" corrected.

Richard West <r.west@neu.edu> then merged the commits, removed redundant changes that 
confused the diffstats, and wrote the following description.

The net result seems to be

* Cyclic_Ether_Formation:
	New groups so that the top level can match RnOOR as well as RnOOH
    New rules to fill in some data for these new groups.
	Unfortunately the default diff formatting for me makes it hard to see if any of the
	original data were changed, because they are compared against the new data.

* HO2_Elimination_from_PeroxyRadical:
	It is given a reverse name: "HO2_concerted_addition"
	9 new rate rules added.
	Unfortunately these come with very little information about where they are from
	or who did the calculations, or what the species were. (Does "sp, ts, tt, etc. mean something?)
    As we have space to store this metadata, it would be good to add it.

* R_Addition_MultipleBond:
	2 new groups as sub-groups of O_rad/NonDe
	(Irritatingly causing all the other groups to be renumbered. Do we use these numbers?)
	9 new rate rules added.
	Again, these come with very little information about where they are from.

* Substitution_O:
	The Y_1centerbirad group is no longer allowed to be a CO atom type.
	I have no idea why not. Perhaps there's a commit message in the RMG-Java project.

* H_abstraction:
	These changes were reverted, but it looks like there have been some in RMG-Java
Added USC-Mech-ii thermo library.

This is the first concrete output from the chemkin importer project.
Fix H2CC electronic state in USC-Mech-ii thermo database.

We'd attributed it to the triplet, based on the reactions,
but this is the thermo for the singlet. 
(We should have an inter-state crossing reaction in our models)
importOldDatabase.getUsername() now works on posix systems without os.getlogin()

This solves a problem when running on one of our clusters, which would 
otherwise give an OSError when you try to call os.getlogin()
Tweak a comment in R_Addition_MultipleBond/training

When this is exported to RMG-Java style database, it became ambiguous.
(It said "THIS is the full rate not the per-site rate" but that was 
no longer true, because the comment was re-used on a rate-rule which
has been translated into a per-site basis.)
exportOldDatabase.py removes heteroatoms from thermo libraries.

Some thermo libraries contain nitrogen atoms, which confuses RMG-Java.
This prunes those species, so the exported database can run in RMG-Java.
Currently it only allows C,H,O and S through.
Script for converting RMG-Java individual kinetics libraries to Py format.
Added Cl2, Cl, and HCl to primaryThermoLibrary from Burcat Thermo Database.
New Entry: R_Recombination/training/1

Rate rule for CO[O] = [CH3] + O2

Submitted through the RMG website.
New Entry: R_Recombination/training/1

Rate rule for CO[O] = [CH3] + O2

Submitted through the RMG website.
New Entry: R_Recombination/training/2

Rate rule for CCO[O] = C[CH2] + O2

Submitted through the RMG website.
New Entry: R_Recombination/training/3

Rate rule for CCCO[O] = C[CH2] + O2

Submitted through the RMG website.
Use RMG-Py's native addition of training reactions to export rate rules.
Fix bug of added training reactions not using correct atomLabels.

atomLabels must obey original family template recipe.  Even though
these reactions are in the reverse direction of the reaction family,
the * tags must still be used for the reaction in its forward form.