Using tags! My suggestion is the option to tag a pdf. It is much more intuitive. Doesn't matter were you saved it. Easy to locate.
Creating tags is the way the note softwares use to organize tons of information. Have you noticed how easy is to find a note in Evernote? My suggestion is to let people add a tag to pdf. If when you are reading you tag one or many words by clicking a tag icon, then you don't have to move the file or worry to remember which folder you saved it. You may have 500 pdf’s, but tags you created will guide you to find what you need. Please consider it.
For example, a article about a new medication that treats hypertension, I could tag medicine, hypertension, drug. When I'm back to the software, if I click one or more tags, that software finds all pdf that have those tags I created. Impossible to loose a file. Don't waste time saving it. Just tag while reading. .. It is just so much better and more complete than favorites.
Great if it could edit the standard document tags, readable in any device and program!