Split of Benchmark and Permutor Tool

• no longer have the option to allow duplicate vmaf scores (was kinda pointless)
• benchmark tool & permutation tool are split out into their own tool for clarity
• benchmark tool supports both one-click execution, and cli run functionality
• readme updated to reflect the new changes
• removal of reference files as they are probably out of date
• heavy splitting of shared code into sub-modules for easier unit testing and separation of responsibility