-report-duplicates warns when multiple choices exist for the same bonded interactions

Added the "-report_duplicates" which warns the user when multiple bonds, angles, dihedrals, or impropers were automatically generated for the same set of atoms. This kind of ambiguity occurs frequently. This is especially important for the upcoming 2023 version of the OPLSAA force-field, which contains many duplicate or ambiguous bonded interaction definitions.

This feature makes it possible for users to find out when other possible bonded interactions exist. If so, they can override the default choice manually.

This feature is probably not very useful unless you are using the 2023 version of OPLSAA force field (which has not yet been released).