Just had quite a success with Xournal:
http://www.g-loaded.eu/2008/05/03/how-to-annotate-pdf-files-in-linux-using-xournal/
http://xournal.sourceforge.net/
"No one said that annotating PDF files in Linux is an easy task. I
have tried many open source tools for that job, but xournal seems to
be the best one at the time of writing."
I believe that his recommended setting:
startup_ruler=true
is now:
highlighter_ruler=true
The weird "thickness" values are specified in "points" (1/72"):
highlighter_thicknesses=2.83;8.50;19.84
These are 1, 3, and 7mm respectively. I've experimented with point-sizes
of 5.6, 8, and 11. Time will tell whether these are a good idea or not.
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