Clean up gmx insert-molecules

- Remove unnecessary code.
- Clarify control flow and responsibilities of different functions.

The only functional changes should be that:
 - Random numbers are now used in different order because of some
   reorganization.
 - The insertions happen at a slightly different place even with the
   same random numbers (now the generated random number sets the center
   of the inserted system instead of corner location).
 - The insertion positions are equally likely everywhere in the box,
   instead of a somewhat arbitrary rejection criterion that rejected
   some positions at the edges.
 - The -allpairs option is gone.
Child change will provide a proper fix for the latter by getting rid of
the mdrun-specific neighborhood searching and all the memory leaks that
the code in addconf.c brings.

Change-Id: Ia82ebb8ea8296dd468a9a56c33a3cb737a5ec9dd