More Robust Input Parsing

[brrcrites]

Need to create a more robust and logical input parser that is better attuned to different input cases and is less likely to break because of small errors in input files.

[brrcrites]

We may want to consider converting the readers into their own classes so we can make the main a bit more straightforward and extensible (although idk if anyone is going to have any other input file types, but could be useful to someone or at least make the reading more re-usable).