Merge branch 'candidate-1.1'
removed raw_pairdiffs
Put the declarations of bruvo dist on one line.
initialized doubles for bruvo dist
More comments, arrangement of poppr_distance.c
R_Calloc is working (so far)
add notes
made sure to use R_Calloc for allele_array
resizing genotypes complete.
Fixed issue with expected values switched.
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.