Bug fixes

[cjneely10]

This pull request provides small bug-fixes and updates to EukMetaSanity.

As the changes constitute a small change in output, this PR will qualify as a SemVer minor version bump (and not just a patch).

Notable changes:

• Better installation experience
  • Handle partial installations
  • Uninstall flag
  • Upgrade flag
  • Clientside binary directory generation
• Optimized Augustus runs
  • First-pass uses GeneMark output for first Augustus model, or defaults to legacy behaviour
• Fixed taxonomy parsing algorithm