The input, location, code thing and the hall, shelf, box thing are the same thing... I think, it's been a while but I'm pretty sre that's right.
There are some folders with numbers on the right side, those are not dates. They'll be on a format like "99/99/99" (kinda like dates, but... they're not), you input them onto the machine thingy and new documents will appear on the table below the big window. Click on it, drag and read the files and solve the mystery!!
I can take a screenshot if you're still having troubl :D
Or explain it further if you don't want spoilers ^_^