Major rewrite/refactor of codebase. Still needs test cases.

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>
Refactored FileLineSplitter to remove code duplication.

Also includes small fixes in Submission (bug where files were not being matched).

Small copy-and-paste error in SimilarityMatrix fixed.

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>