Initial manual and documentation update
Merge branch 'master' of https://github.com/shirtsgroup/InterMol
Revert "Merge branch 'master' of https://github.com/shirtsgroup/InterMol"

This reverts commit c04d987b1e444edbf8e54ec6c32adce56dbff681, reversing
changes made to 8f08dc7098068c99b35eddc2209945d2ec3b2d0f.
Earliest stages of desmond reorganization, still working as it was - more drastic changes in progress.
Further changes to desmond parser, fixed lammps examples
Partial removal of regular expressions, simplification of logic.
First half of logic reorganization
Fixed most of a pairs writing issue, more reorganization.
Small fix to dihedrals
Desmond reorginization complete (for now), currently needs to support canonical and LJ-14 is off.
Breaking up the write functions and generalizing bonds.
Merge branch 'desmond_reorg', remote-tracking branch 'origin' into develop

Resolved data conficts with:
validation/inputs/Lammps/UnitTest/bond_style-none/bond_style-none-data.lmp
validation/inputs/Lammps/UnitTest/ethanol_no-dihedrals_hybrid-bonds/ethanol_no-dihedrals_hybrid-bonds-data.lmp
Fixes for desmond writing split into functions.