There are some great ideas here - has anyone given some thought as to how to make this work with zotero? (
www.zotero.org) Since Zotero stores its files locally (and can be run on a USB drive with portable apss firefox).... maybe one possibility could be having everything run off the USB drive only?
Taking this much further than my tired brain should right now- zotero (free software, you should take a look if you haven't seen it), uses a flat file system with sqlite. I assume the squiggles can be created in the same directory as the PDF automatically. Merging would be simply running through the PDF directories and looking for squiggles and merging them. Backup would be straightforward as backing up the USB drive. If you don't want them merged, editing the sqlite file indepedently is theoretically possible, or just manually adding it to the zotero database.
Manually finding articles on the USB drive may be a bit of a challenge, but some of the ideas posted here may resolve that side. Some type of automatic parser should be straightforward.
