Adds two new options + several fixes

[gibbbone]

I added two new CLI options mostly because they were useful for my use case, but I think they're improving how the script works for everyone.

tex_folder makes possible to specify a .tex subfolder where to look for input files other than the one where the main file is present.

interactive for any input file asks the user if he wants to include it. I used it to avoid inserting the Appendix in the main file.

I have also updated the README with explanations and done some cleaning on the functions.