Reorganizing commands for annotate and "full".

[emarinier]

Note: merging into dev/annotate instead of develop. Mostly as a way to contain all the annotate stuff while we work it out.

Added:

• cmd_annotate: which will be used for annotation in the future
• cmd_full: which will chain cmd_assemble and cmd_annotate into a single command

Changes:

• Much of the code in cmd_assemble and cmd_evaluate have been moved to a corresponding pipeline. This helps make the code reusable for cmd_full.
• The assemble pipeline now returns the file path of the assembled contigs, which is helpful for integrating it with cmd_annotate.
• Refactored some redundant filepaths into config.py instead of repeating the same declarations.
• Updated the related tests as appropriate.