Database clean up

-Add depository.py and training.py for new reaction families.
-Add many histories to entries using git blame
-Add duplicate=True to one reaction in OxygenSingTrip.py
-removed Sulfur/thiophene kinetic library. There is a mistake in the
library (probably an improperly copied adjlist) and the original authors could
not remember what is correct. We elected to just remove it from official
seeing as nobody in the group uses it.
Fixed more history on groups and libraries
Convert kinetic libraries to give 4-column adjlist

Performed by loading and saving the entire database.

Many kinetics
families were reshuffled and for some reason all scientific notation was
changed to non-scientific notation. Did not commit any changes to families
in case something more damaging happened
Update adjacency lists to 4 column format
Update adjacency lists to 4 column format in PrimaryTransportLibrary
Update adjacency list in GRI-Mech transport library
Cyclic_Ether_Formation: Update adjacency list with explicit lone pairs
H_abstraction: Update adjacency list with explicit lone pairs
HO2_Elimination_from_PeroxyRadical: Update adjacency list with explicit
lone pairs
intra_H_migration: Update adjacency list with explicit lone pairs
R_Addition_MultipleBond: Update adjacency list with explicit lone pairs
R_Recombination: Update adjacency list with explicit lone pairs
Cyclic_Ether_Formation: C#O and update adjacency list with explicit lone
pairs

- update reaction recipe for C#O (carbon monoxide with triple bond)
- update adjacency list of C#O for triple bond
- add explicit lone pairs
combuction_core version2: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
combuction_core version3: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
combuction_core version4: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
combuction_core version5: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
Dooley C1: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
methylformate_2: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}
Dooley methylformate_all_ARHEbathgas: Update carbon monoxide to C#O

- update the adjacency list of carbon monoxide to triple bond (C#O):

1 C 0 1 {2,T}
2 O 0 1 {1,T}