Moltemplate

1) Fixed bug preventing "pair_coeff" commands from being understood correctly if they appear outside of the "system.in.settings" file (ie. outside the "In Settings" section). (This is the place where those commands usually appear.) Now "pair_coeff" commands can appear in any file created by the user, and they will be post-processed correctly (even if the atom-variable-names contain wildcards).
2) Made some additions to the moltemplate_manual including a new chapter on creating (and using) force fields.

fixed a bug preventing generation of helpful error messages in response to non-sensical user input (eg "atom:"). The previous version would crash with an uncaught exception when presented with this input:

write_once("In Settings") {
pair_coeff atom:WallParticle/W atom:
}
Molecule {
write("Data Atoms") {
$atom:w $mol:. atom:W 0.0 0.0 0.0 0.0
}
}

(The syntax error in this example is on line 2. The new version of ttree.py and moltemplate.sh generate error messages instead of crashing.)

fixed a python3-specific bug in ttree.py causing expressions containing ".." (like "atom:../A") to sometimes cause an uncaught exception. Example:

MoleculeTypeA {
write_once("In Settings") {
atom:../A
}
}
MoleculeTypeB {
}

These kinds of expressions should work again now. (The A leaf node should be created in "/" now.)

updated the manual. updated dump2data.py. fixed a bug reading triclinic boundary conditions from PDB files that affects some versions of awk. Corrected the README file for the EFF example.

Previous versions of **genpoly_modify_lt.py** would crash when told to make 0 modifications. The current version handles this edge case more gracefully. Several examples and README files were also updated.

fixed a bug in COMPASS and "msifrc2lt.py" causing low priority dihedrals and impropers to occasionally override high priority ones