command line arguments should follow the same syntax

[seasidesparrow]

Currently, argument calling options use a mix of dashes and underscores. These should be standardized to one or the other.

Current options are:

• --match_to_pub (change to --match-to-pub)
• --match_to_eprint (change to --match-to-eprint)
• --data-path
• --add-to-oracle
• --query-oracle
• --number-of-days
• --output-filename
• --list-source-score
• --apply-source
• --matched-file
• --cleanup