v1.4.0

This release includes commits that:

• Hybrid tip labels now have '+' added to them in the dup-counts output
• Re-factored code
• Removed -d and replaced with the --st-only and --no-st options, which seems clearer
• Clarified how -v works
• Converted underscores in output files to hyphens
• Changed format of output files (see website: https://gwct.github.io/grampa/readme.html)
• Added -scores.txt that contains score information for all MUL-trees rather than just putting that in the .log file
• Converted global vars into a dict