also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases

allows deleting of a user-specified set of atoms, based on topology

also, fixes a bug introduced in PR #1189, when not using stabilization

enables consistent syntax when using custom groups

thanks to Sagar Patil for report

option to update all atomic charges, even when edge atoms are defined

now always throws error if a bond type changes, but both of of the involved atoms are too close to edge of template

- in fix rigid, rigid/small, and poems, a string argument was
  incorrectly assigned to a %d format
- plug two small memory leaks in fix bond/react

fixes crash e.g. when building on Ubuntu for Windows
thanks to Márk Jenei (University of Cambridge) for submitting error report