Added print statements for distance matrix.
added else statement
Differing print statements.
verbose genome addition
added logic to Infinite model
added test function for mindist.
Changed the construction of the distance matrix.

The distance matrix was filling up in the wrong way and corrupting the calculation of the genome addition model. This was caught only when properly allocating the memory. This works now, but I will have to run through everything to make sure that things work as expected.
properly calling short_inds

This fixes the issue that UBSAN detected.
Dealt with zero_ind memory allocation
beginning cleanup.
removed print statements
Added notes.
Added note about bug fix