Standardize CLI argument names

[jkirk5]

Desired capability or behavior.

Currently the various utilities were written at different times by different people, resulting in slightly different arguments for each command. For example, sometimes specifying a legacy code is done with -l, but in other places it is -f.

Commands should be standardized across Aviary, with identical naming scheme for similar concepts, as well as ensuring things like which arguments are positional are also standardized (meaning standardizing things like aviary command input_filename -o options vs. aviary command -f input_filename -o options)

Is your feature request related to a problem? Please describe.

No response

Associated Bug Report

No response

[xjjiang]

This change will affect doc building. Hopefully, glue feature can help but still we need to manually update the docs.