Flagged out part of the code that didnt do what it was supposed to do
 It tried to find 2 adjacent radical sites and make a double bond between them
 However, there is no cycling over the different resonance isomers
 and nodes are not updated after they have been changed making the new graph identical to the first graph
 A working code doing the same has been written long before in the generateResonanceIsomersFromRadicalCenter() subroutine
 but was flagged out due to wrong thermo for birads and unwanted reactions
Skip checking for the stablest resonance isomer once thermo for initial graph
is obtained from a thermo library.
Bug-fix: resonance isomers always include the original molecule when they exist and only then
This made the new conjugated ring code to add various similar species, as in this case only the resonance isomer
was added to the resonance isomer vector.

This also relates to previous commit: when resonance isomers existed, it was checking all of them for lowest thermo
unrelated to the fact if the original thermo was obtained from a library.
New change that might speed up the code a little bit in cases a lot of non-resonating radicals are present.

Old code always added the radical to a new resonance vector, while now this is only done when a first resonance isomer is found.
This can help bypassing some checks if(resonanceIsomers = null) speeding up the code and requiring less mem.
Added rate coefficients for the intramolecular exocyclic addition R6_SMS_D
New rates for 1,3_Insertion_ROR. Significantly slowed down the alcohol eliminations and added a value
for H2O elimination in ipentanol.
The new endocyclic addition tree. Reorganized the tree in order to allow the calculated values to get
priority level 5. I also added some estimates and calculated values to block strained reactions.
The new exocyclic addition tree. Again the tree needed some restructuting in order to allow the tree to be filled
up by estimates. I added some estimates and calculated values to block some steric hindered reactions.
Added two new rate rules for reactions involving the CdsJ=Cdd group
Reported rates were too high.
Added some rate rules for addition reactions involving the Cd_allenic group
Nist + estimated values
Added the Cd_allenic group to the tree and dictionary for the recombination reactions.
Small update of the intra_disproportionation reaction family. Slightly slower rates for conjugated systems.
Fixed bug in R addition multiple bond.
Cds-H_Cds-H => Cds-HH_Cds-HH
Added a new estimate for the R_Add_Multiple bond Ca_Cds-HH + CdsJ=Cdd
More helpful message for Pdep failure

My jobs suddenly started failing while running pdep jobs,
this was because one of the libraries I was using had
irreversible reaction. This commit will give a more helpful
message when it fails.

Irreversible exit channel is typically allowed in pdep codes
like variflex, I am not sure if we should just check for
whether reaction is irreversible and only then try to reverse it.
Or make an irreversible reaction also reversible in order to
maintain thermodynamic consistency (?).
Merge branch 'master' of github.com:GreenGroup/RMG-Java

Conflicts:
	databases/RMG_database/kinetics_groups/1,3_Insertion_ROR/rateLibrary.txt
	databases/RMG_database/kinetics_groups/Intra_R_Add_Endocyclic/dictionary.txt
	databases/RMG_database/kinetics_groups/Intra_R_Add_Endocyclic/rateLibrary.txt
	databases/RMG_database/kinetics_groups/Intra_R_Add_Endocyclic/tree.txt
	databases/RMG_database/kinetics_groups/R_Recombination/rateLibrary.txt