CLI-defined input and output paths

[hyperrealgopher]

Ignoring the path variable from the CLI and just using the INI to get the output directory and input directory.

Need to either drop CLI support for defining the input and output path and compeltely rely on the ini file, or completely implement support for the CLi args.

This may also go hand-in-hand with adding a config abstraction, because then the config abstraction could have its output/input entries changed early on before it's passed around. Related: #20

[hyperrealgopher]

Dropped CLI support for output and source directories. Need to reimplement.