Use CLI in Otter Grade to override configurations in `otter_config.json`

[chrispyles]

Currently, many configurations need to be specified twice (once in the otter_config.json and again via the CLI) to be properly handled. For example, grading ZIP files or exporting submission PDFs.

This should not be the case, and CLI flags should be used to correctly set configurations in the otter_config.json.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[chrispyles]

As part of this refactor it would also be nice to remake the Docker image build process so that changing the test files/support files doesn't require re-building the Docker image.