Rename final synteny block output, tweak collinear merging

[lcoombe]

• Rename final synteny blocks to be more clear
• Add --force option, which will run all snakemake rules, regardless of the output files that exist
• Had added a tweak that allowed collinear block merging over small blocks (less than -z) to not disrupt the contiguity
  • In larger tests, I found this aided in contiguity, but negatively impacted the correctness
  • Because I'm erring on the side of caution, removing this tweak from ntjoin_synteny.py
• Bugfixes, code clean-up