Add the Ability to Keep Individual Files and Filter the Files List

[loren138]

• Adds the ability to keep the individual PDF files around and export details (useful for later combining).
  • I have a custom utility to bind in a table of contents, outline. Sadly, it's Swift/a mac binary so not generally useful as part of this project, but it is public https://github.com/loren138/mac-pdfnup
• Adds the a filter function to allow filtering out certain files

If you ignore whitespace changes in the diff, it will be smaller. (I added an if statement for exporting the combined PDF which changed several lines.)

Also, I added a good number of lines to the readme.