xournal

is currently the only open source note-taking software that has top-notch annotation facilities for pdfs (and images), that works on Windows, Mac, and Linux. It is the default pdf reader on all my machines. I have tried Skim (Mac), Okular (Lin/Win/Mac), and a few others. Nothing comes close in interop, customizability, and features. Plus, your notes are stored in xoj files that are simple to edit and save and sync.

current status:

compiles & works for me on ubuntu 12.04. uses poppler 18 that breaks previous code. my last working version for poppler 16 on ubuntu 11.04 is tagged pre-poppler-19.
some iterations before that should work with OSX 10.6.4, 10.5.8. install deps with MacPorts ( sudo port install xournal ), and replace the MacPorts xournal. as of 2011-02 untested and you’ll need some extra libraries
libgcrypt11-dev + libsqlite3 for bookmark function

contains these modifications:

select text, create a highlight box & copy selection to clipboard

popup dialog after select to confirm copy to clipboard
search for 0x40409040 in xo-paint.c (in start_selecttext) to change select box color

auto save and load last opened page

when you open a pdf, xournal will jump to the last viewed page (unless overridden with dmgerman’s page number command line argument). requires sqlite3-dev and libgcrypt11-dev. stores and reads ~/.xournal/xournal.db

manually editing .xoj files

if you are interested in editing .xoj in vim, add these lines to your vimrc (requires gzip support):

autocmd BufReadPre,FileReadPre    *.xoj setlocal bin
autocmd BufReadPost,FileReadPost  *.xoj  call gzip#read("gzip -S .xoj -dn")
autocmd BufWritePost,FileWritePost    *.xoj  call gzip#write("gzip -S .xoj")
autocmd FileAppendPre         *.xoj  call gzip#appre("gzip -S .xoj -dn")
autocmd FileAppendPost      *.xoj  call gzip#write("gzip -S .xoj")

other update list

2011-01-31 safe pdf backgrounds with relative filepath if same basepath found
2011-02-01 added image extraction. copy to clipboard after text selection will now automatically save a png of the selected region; the png filename is written to ~/.xournal/extract.log for hook use
2011-02-01 executes the file found at ~/.xournal/hook-post-extract if it exists
2011-02-05 actually create an undoable rectangle item where text-selection was used; mostly copy pasta from the stroke
2011-04-07 added files and modifications for nautilus thumbnail support by russell sears
2011-04-09 adding auto-bookmark and restore last-read page function

more generalized changelog

2011-01-31 changed selectRect code (swap y1 & y2), somehow this makes selection more correct
2011-02-05 looks like it segfaults if there isn’t a background pdf?

whacked/xournal_fork_dmg