Social Science Statistics Blog

You may be interested in PDF-Xchange, available free from Tracker software. Available here:
http://www.docu-track.com/home/prod_user/PDF-XChange_Tools/pdfx_viewer

It fulfils most of the criteria you list, and I've found it very useful. However, it seems to be windows only.

the "it seems to be Windows only" part unfortunately is a killer...
The lack of a pdf editor for linux is the biggest (and perhaps only serious) problem with linux I currently see - by now I'd even be willing to pay a couple of hundred bucks for an adobe, but they only have the reader for Linux.
There are currently two programs that claim to work as pdf editors - pdfedit http://sourceforge.net/projects/pdfedit
and cabaretstage
http://www.cabaret-solutions.com/en/products/stage

unfortunately both are terrible and useless I recommend you stay far away from them.
Everything _but_ annotation (i.e. deleting pages, joining documents etc. works great with the multivalent tools, which work great:
http://multivalent.sourceforge.net/Tools/index.html

Have you tried Okular?

http://okular.kde.org/

I believe it comes closest to your list of criteria. But it is still rapidly being developed, so you could also email the developers about anything that you find lacking. My main beef with it is that it renders some LaTeX math symbols poorly.

Preview on the Mac (free with purchase of a Mac) does all you've requested, except the multi-column copy and paste doesn't work perfectly.

I am sure other Mac evangelists have told you Mac's OS X is built atop UNIX, and thus most if not all of Linux's command-line-control goodness is available on the Mac. If it's other free open-source software you like, there's plenty for the Mac.

Not convinced yet? Have a look at the journal article management tool Papers, available only on the Mac ...

http://mekentosj.com/papers/

Thanks for your suggestions, all! In order:

-X-change does seem quite nice; the free version does everything I want, and I'll recommend it to others, The Windows-only thing is kind of a killer for me though.

-Okular has the free and the Linux down great, and I just found the annotation tools (as I think they're new to qt4, but I'm not sure.) Only problem is that the changes aren't portable, they're stored in metadata that's hidden from the user.

-Mac stuff may be portable in theory, but most of the software is built on the Cocoa Objective C toolkit, isn't it? Tough to find out how that converts.

It looks as though the best Linux options don't alter the PDF file itself, and the ones that do (pdfedit) are unreliable for basic annotation...

I'm going through similar issues. I'm a linux guy myself, but have unfortunately had to give it up for my tablet laptop. Linux just doesn't have all the support to edit pdf's yet. It has some nice features like the wacom support to draw with, but note taking in general is not "done" for any platform. What I really think will be killer is when apple releases their tablet which I think will be the most intuitive way of editing pdfs. But I bet it will cost some serious $$.

@Andrew, you are adding criteria :) but it is a fair point. One mitigating factor is that qt4 apps can also be installed on Windows and Mac, so the files should at least look the same on all platforms. Also, KDE4 has an advanced system for accessing and handling metadata called NEPOMUK, but I am not sure if it is finished and in any event, I haven't fully grasped its potential, but it is something to be on the lookout for.

@Nick, have you tried Xournal?

http://xournal.sourceforge.net/

It is my favorite note-taking application on a Linux tablet PC and IMHO works perfectly for marking PDFs (if you have a stylus; my guess is that using it with just a mouse would be annoying). I actually like it better than any note taking app I ever used on Windows, but thankfully I have been Windows-free for a couple of years now so I don't know the current state of Journal, OneNote, etc.

In my first comment, I complained about Okular's rendering of some LaTeX math symbols. It appears that problem has been solved in the current beta version, so complaint officially retracted.

I read around a bit about PDF-Xchange. It does seem to offer annotation, but reviewers complain about the free version leaving watermarks on the pdfs. Is it true that you have to get the paid version to avoid them?

On Windows, try Foxit, http://www.foxitsoftware.com/pdf/rd_intro.php. It includes some basic editing features like annotation in its free version, although it may leave a watermark.

On Linux, you can try PDFedit (http://pdfedit.petricek.net/index_e.html). However, it probably has more editing features than you want and is less user friendly than Acrobat.

The GNU foundation is making a push to develop a free PDF library and reader/editor - http://gnupdf.org/Main_Page. It is still under development, but when it comes out, it should be good.

To get multicolumn text out, try using pdftotext (included with xpdf - http://www.foolabs.com/xpdf/) on the command line with the -layout option. Something like,

$ pdftotext -layout foo.pdf foo.txt

This will create a text file with all the text from the PDF. The layout is preserved, so the multicolumn text that you want should still be columns and you can copy it from that.

Allow me to add to your wish list:

ability to share annotations with others!

In fact, I liken the pdf format to the fax: useful for a time but fundamental a dead-end technology. Academic papers should really be more like wikis than pdfs; they should track changes well, and they should allow for multiple views of annotations of scholars around the globe.

In the meantime, good luck on your more practical search for a pdf-plus product for linux!

I just remembered that when I actually did once use a free pdf annotator. It is open-source. It actually worked fine for me, but it saved your annotations to a file separate from the PDF rather than to the PDF itself, which bugged me enough to stop using it. It may be worth trying though. It is called Jarnal and is available here.

http://www.foxitsoftware.com/downloads/

foxit is developing a linux version and there is a preview for it on the foxit website. The program work wonderfully in windows.

I run Foxit reader for windows in Wine on Ubuntu and it works brilliantly.

The linux version didn't run well at all, and has a different and less useful interface.

Perhaps I missed the meaning of your title altogether, but I think you should have used "whence" instead of "whither".

Have you considered online collaborative writing tools? Docs.google.com is an option, and there are many others. Is it that the online collaborative writing solutions are too limited?

Thanks
Justin

For Mac users, the best option out there is Skim.

http://skim-app.sourceforge.net/index.html