Added flags to start execution from files, save traces of runs.

Modified initialization such that it can start runs from files. Added flag for saving intermediate ratios to file. Save intermediate code to file. Format of outputted c code has been changed. From generated-[idx] to generated-[test_name]. This was done because we might only run a subset of tests or we might run them out of order. To determine which tests were run we don't need to check info.csv anymore