pair_coeff commands can now appear anywhere

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.