After years of waiting for a top-quality open source PDF editor/markup tool, and being baffled why they don’t exist… I’ve given up. What I’ve settled on for the moment performs rather well:
At a command line, I type
pdfedit <pdffilename>
You can download my pdfedit, which is a file in my ~/bin folder (which is on my path). It relies on closed source Windows software (!agh!); see http://www.tracker-software.com/product/downloads, installed in Wine.
Essentially, it opens the given pdf file in Tracker Software’s editor, which makes highlighting and annotating easy. I will probably stop printing out papers completely now, even though I tend to prefer reading and marking them up that way, as the paperless filing system is too much of an advantage.
I use the same key for pdf filenames as I do for BibTeX key names, and have the following bash function to search for them:
bibgrep()
{
grep --ignore-case $1 /home/cpbl/texmf/bibtex/bib/*bib | grep -iv "abstract=" | grep -iv "abstract ="
ls ~/web/publications/*pdf ~/library/*pdf ~/library/*/printed/*pdf ~/library/*/printed/*doc ~/library/*/*doc ~/library/*/*pdf | grep --ignore-case $1
grep --ignore-case $1 /home/cpbl/library/listOfPrintedFiles.txt
}
The Red Pen 