I was initially stumped by this PDF-folder issue. I decided to keep my master copy of my library on my USB (CF in your case) and then back that up regularly. When I get a new article I download it to the PC (because that's what I use for searching) and decided to write a little script that:
i) creates a PDF container folder,
ii) writes a manifest.xml file
iii) includes an image of the front cover of the journal
iv) allows me to enter the title of the article so it appears nicely in the contentlister
I then move that container to my library on my USB. I then see the article with the full title and an image of the journal cover so it looks "pretty" and helps me to remember the article.
I was nervous about doing this at first, but I use rsync to do quick back up my USB key on a regular basis and it works fine for me. It is simple to plug the USB into my PC if I want to view an article on the PC or print it (but this is rarely necessary).
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