Resolve "Refactor file up- and download"

What does this MR do (summary)?

Closes #51 (closed), #56 (closed)

• Paths are no longer assumed to be relative
• All paths can now be configured through the application.yaml
• Single files are no longer zipped
• Downloading multiple submissions is no longer a zip of zips, but rather just directories in a zip
• Downloading multiple submissions now gives a zip in the following format:

submissions.zip
    assignment_1/
        group_1/
            submission_1/
                file1.s
                file2.s
        group_2/
            submission_2/
                file.txt
    assignment_2/
        ...

Does this MR meet the acceptance criteria?

• The main application was run to make sure the server still runs without errors.
• Tests were written to verify the behaviour of this code.
• Javadoc and other comments were added to make the code understandable.
• The code adheres to the style guidelines.