Master PDF Editor
The linux version of this software is free and closed source. It will not run on Debian Wheezy, as it requires glibc >= 2.14, whereas Wheezy has version 2.13. You can either pull in a newer libc from testing, or simply use testing (Jessie). See here for how to use glibc > 2.13 on wheezy: http://verahill.blogspot.com.au/2014/03/562-pulling-in-glibc-214-from-testing.html
So I tried it on Jessie.
While it almost works, I can't prevent the program from screwing up the fonts in the process. Also, the annotations don't show up in acroread for some reason. Saving as PDF/A didn't make any positive difference.
|The annotation shows up in evince -- but the font's weird now|
|Same goes for Xournal|
|In acrobat reader before editing with Master PDF Editor|
|in acrobat reader after adding an annotation. The annotation doesn't show up, but the fonts are screwed up.|
So we're almost there -- Master PDF Editor does everything I want in terms of PDF annotation, but at least on linux there are issues with the fonts in the resulting PDFs.
I, Librarian is both free and open source. It claims to be web-based -- which is true but can be misunderstood. What it means is that it is browser-based and runs a server on your computer. My first thought when I see 'web-based' is that I'm handing over my data to someone else, but luckily that's not the case here.
I installed the .deb file meant for ubuntu.
Using I, Librarian is quite straight forward, but I could not see the annotations in any other program that I tried, which makes it of little use for me -- I make annotations in galley drafts for journal editors, and for students to give them feedback on latex documents.
Either way, to start, just go to http://127.0.0.1/librarian
Make sure to edit the settings to make I, Librarian use the internal pdf viewer in order for editing to work.
No matter what I did, I could not export my pinned annotations though. They did not show up in either evince or acroread.