Centralize code

[jmtsuji]

Related to comments on #1, I generalized several parts of the code in repair.py and moved them to utils.py or rotary_utils.py. This should make rotary-utils more extensible and also overcomes some previous issues with logging.

Summary of changes:

• All logging setup is moved to main of rotary_utils.py, including console loggers and file loggers
• Two files loggers were added: one writes a log file to the output directory if a utility specifies an output_dir where all outputs will be saved. The second one writes a log file to a custom location specified by the user.
  • This restores the lost log file functionality in #1
• Arguments that will be common to all modules were moved to a parent CLI parser in rotary_utils
• Some parts of main in repair.py were moved to utils.py and rotary_utils.py, including setup of the output directory and checking/reporting of dependencies
• Minor enhancement: metavars were added to the CLI parser for clarity
• Enhancement: add reporting of dependency versions in log

@LeeBergstrand I hope this addresses the previous comments in #1. Look forward to your review.

[jmtsuji]

@LeeBergstrand As you mentioned, I'm going to go ahead and merge in this PR to develop, and then we can do a fuller code review there. Thanks!