Merge dev/summaries into develop

[emarinier]

This merge request adds features relating to summarizing the assemblies. The related project is: https://github.com/proksee-project/proksee-cmd/projects/4

Added:

• Summarizing the "final" assembly in the same way as the "fast" assembly.
• Creating a CSV file summarizing the assemblies run.

Changed:

• Cleaned up program output.
• Large amounts of code refactored into more appropriate files. Primarily from the expert system class to the assembly evaluator class.

Note: cmd_assemble is overdue for refactoring, but I felt that it was outside the scope of this feature branch, so I left it for a later time.