Implement input function to handle skipped files and check ouputs and header

[yucongalicechen]

• For lists and globs, the best behavior would be to read as many files as possible and skip over the others, letting the user know which have been skipped.
• We would like to have tests for all the same sets of inputs that were used in user input files UCs #48 and input file list #55 but that check that the right correced files are written to the right places (so glob the directories after the corrections are applied and check the list is as expected).
• Also, let's make sure that the args that are written to the file headers are correct, where the parent file is correctly identified (i.e., not just the input file list saved to the header, but also the actual file that was used for that particular correction. This will have to be set inside the loop).