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Breaking changes:
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* `--output_directory` is now mandatory, don't create a default output directory in data/<today's date>
* Upper limit for the `--run-id` argument down from 99999 to 9999
Non-breaking changes:
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* Process all the files in a directory as multiple input files through the new arguments `--input-directory` and `--output-directory`
* New `--move-input-files` argument to move the input files to the output directory after processing
* New `--run-id-file` arguments to read and save the next Run ID. Allows for automated recurring runs, for instance associated with the `--input-directory` and `--move-input-files` arguments
* New `--input-encoding` argument to specify the encoding of the input files, defaults to 'utf-8'