This advice appears many times here, in many forms. Here’s one instance:
@wajakob asked this in the context of “organizing my research files while getting ready for a new project.” Don’t ask Tinderbox to organize your files. Use Finder, or if you want to spend money, then use EagleFiler, or the Cadillac, DEVONthink. Those are purpose-built to organize files. Tinderbox is not. It’s an XML file. Stuffing binary versions of files into an XML file is not efficient.
But certainly make notes about your files, link to them, summarize their content, as well as other research notes, in Tinderbox. That’s Tinderbox at its intended best: working with notes, then reworking them as needed, then rework the rework, as your research takes form and approaches the goal.