Added Some of the JP10 Libraries
Finished Adding JP10 Libraries
Libraries for v0.7 of JP10 added
Added JP10 Pyrolysis kinetics libraries and modified others.
Turn off certain families for JP10 model building.
Added more species to CPD thermo library.
Changes to database made by Aaron Vandeputte.
Merge branch 'master' of git://github.com/GreenGroup/RMG-Java into jp10
Added new reaction family Intramolecular Diels Alder.
Aaron's changes to kinetics groups
Aaron's changes to JP10 kinetics libraries
JP10 thermo libraries update
Aaron's changes to thermo groups
Allow all kinetics families
Added function for finding the closest distance between two nodes
in a graph
Modifications to make intra H migration use smallest ring template.

Temporary hack.  This code may be suspicious.
Fix to minimum distance finder for nodes in a chemgraph.
Changes to the heirarchy tree findMatchedPath which was mutating the path list

Recursive function was appending new heirarchy tree nodes onto path list
inappropriately.  Hopefully this prevents this. This uses a LinkedHashSet
instead of a Stack.  We may want to revert to a Stack to speed things up if
code does not break anything.
Merged Aaron's changes and fixed all merge conflicts.

B bonds in the reaction libraries may still exist.

Also need to clean up Heirarchy tree matchedPathList function
so that we don't switch between LinkedHashSet and Stack.

Merge branch 'aaron' of https://github.com/agvandeputte/RMG-Java into jp10

Conflicts:
	databases/RMG_database/kinetics_groups/Intra_Disproportionation/rateLibrary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/dictionary.txt
	databases/RMG_database/kinetics_groups/R_Addition_MultipleBond/tree.txt
	databases/RMG_database/kinetics_groups/families.txt
	databases/RMG_database/kinetics_groups/intra_H_migration/forbiddenGroups.txt
	databases/RMG_database/kinetics_libraries/JP10BetaScission/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10BetaScission/species.txt
	databases/RMG_database/kinetics_libraries/JP10ManualChanges/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10Pyrolysis/pdepreactions.txt
	databases/RMG_database/kinetics_libraries/JP10Pyrolysis/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10Pyrolysis/species.txt
	databases/RMG_database/kinetics_libraries/JP10rxnlib/species.txt
	databases/RMG_database/kinetics_libraries/JP10seedmech/reactions.txt
	databases/RMG_database/kinetics_libraries/JP10seedmech/species.txt
	databases/RMG_database/thermo_groups/Ring_Library.txt
	databases/RMG_database/thermo_libraries/C10H14/Library.txt
	databases/RMG_database/thermo_libraries/CPD/Dictionary.txt
	databases/RMG_database/thermo_libraries/CPD/Library.txt
	databases/RMG_database/thermo_libraries/JP10/Dictionary.txt
	databases/RMG_database/thermo_libraries/JP10/Library.txt
	source/RMG/jing/chemUtil/HierarchyTreeNode.java
	source/RMG/jing/rxn/ReactionTemplate.java
	source/RMG/jing/rxn/TemplateReaction.java