Allow students to submit directories

[cm090]

The autograder only looks for files in the root submission directory. This works well in most instances but causes lookups to fail if a student uploads a directory with all their files inside. We want to recursively search for files in all the autograder templates, performing the following actions based on template:

• For manual grading, leave the files as-is. Make comparisons on the files themselves and recurse inside of directories if found.
• For automated grading, bring all .java files to the root of the submissions directory. Then use the existing code to move appropriate files into the test runner.

[cm090]

Gradescope has updated their upload workflow to ignore directories. Files are brought up to the root directory before processing.

Submitting directories will work as intended.