Add support for additional flags in main binary

[Chimezie Iwuanyanwu]

Current

Main binary only uses --script as a flag and doesn't support passing in the input/output locations when script runs (handle by config.ini file instead).

Desired

Add parsing of --input and --output flags in main binary to use in both script types. Afterwards, the config used can be specified by another flag --config. All flags can be defined and read from the config file instead of the half and half approach currently done.

[Jhaco]

Added support for overriding config.ini directory values by passing in a directory to their respective flags, and support for running multiple flags/scripts in the command-line.