consider using args instead of input files

[thiagomanel]

For example, we can use something like -criterion name path/to/data function_name arg0 arg1 -criterion name path/to/data function_name arg0 arg1 -criterion name path/to/data function_name arg0 arg1 -o /path/to/output

Note that, we can made available python/bash script to translate our current file based configuration files to this args style

[gabrielfelipeg]

Our current Umbu, Opt and Fast implementation using args instead of input files, only Vanilla still is using input files.