Question: I have a huge collection of PDF. Mostly it consists of research papers, of self-created documents but also of scanned documents.

Right now I drop them all in one folder and give them precise names with tags in the filename.

But even that gets impractical, so **I am looking for a PDF library management application**. I am thinking of something like [Yep](http://www.ironicsoftware.com/yep/) for Mac, with the following features:

* PDF cover browsing (with large preview, larger than Nautilus allows)
* tagging of PDF (data should be readable cross-platform)
* possibility to share across network (thus rather flat files than database)
* if possible: cross-platform

Mendeley seemed to be a good choice, but I am not only having academic papers and don't want to fill it all metadata that is required there.

The only alternative I could find thus far is [Shoka](http://www.mauropiccini.it/shoka/), but the features are limited and developments seems to have stopped already.

Answer: 
I use Docear. Mind-mapping is the mode which I prefer to explore tagged (hierarchical) notes and references. The way they implement hierarchical node trees, it is effectively tagging.

The UI for building out mind maps is fast. Though there is some learning curve to overcome at the beginning, it pays off in spades when you actually index your material in a way which primes your recollection later on. It is the closest thing to augmented memory that I have found besides the Google/Wikipedia/[askubuntu]/etc. combos. =)

<http://en.wikipedia.org/wiki/Docear>
**[Referencer](http://packages.ubuntu.com/de/lucid/referencer)** (GNOME) is a simple tool for managing document collections. 

Tagging is possible.

It tries to find metadata on arXiv or via DOI, but you can add metadata manually too, of course.

But I guess development stopped.