Just so you know, working with PDFs like this is something I only have to do every once in a while, as it’s only when they apply to multiple locations that I need to compare them against each other. Usually we only update one location at a time, or the update applies to a universal document.

Although DiffPDF is a GUI program, if run from a console with two PDF files listed on the command line, DiffPDF will start up and immediately compare them in Words mode, or in Appearance mode if their names are preceded with -a or –appearance on the command line, or in Characters mode if their names are preceded with -c or –character on the command line.
If you’re specifically looking for a command line PDF comparison tool, e.g., for automated testing, try comparepdf.
There are also debugging options. Use –debug to be able to see the zones. Use –debug2 and –debug3 to write the texts in the order they are fed to the sequence matcher into temporary files (e.g., /tmp/page1.txt, etc.). The text reordering is done by the TextItems::columnZoneYxOrder() method in the textitem.cpp file: suggestions for improvement are welcome! (Note that when using –debug3 coordinates are output in y, x order.)

…/Territory 35/Brochure 1.pdf (on the left)
…/Territory 67/Brochure 1.pdf (on the right)

After determining these are the same, I move on to the next PDF for comparison. I click on “File #1…”, select “Brochure 2.pdf” in the dialog, then do the same for the other side. Once I click “Open” on the second side, I get a “cannot compare file to itself” error. Confused, I click on “File #1…” again, and notice I’m in the Territory 67 folder, not the Territory 35 folder as I originally was. It only remembered the location from the last time the open dialog popped up period, instead of remembering the location from the last time I selected a file for that side like I had expected.

I would greatly appreciate it if you could add a checkbox to the Options dialog that read something to the effect of “Remember folder per side” that determines if it remembers one last folder overall (1 total) or one per side (2 total) and is checked by default. In most cases this would be checked, but if e.g. you had to select sequential folders (001, 002, 003, etc.), the end user would uncheck this box so as not to alternate sides.

many thanks