Uploading in case someone finds it useful.

“works for me” on ubuntu 10.10 and 11.04.

• highlight
• freehand markup

• Java runtime
• pdfbox 1.5
• clojure 1.2, clojure-contrib 1.2

easiest way is to install leiningen, run lein deps and have it fetch the jars for you. PDFBox was somehow more tricky; built that first and told lein where to look

• modify pdf-filepath in core.clj or make it a command line argument, then run. it will save an xoj in the same directory as the input pdf file
• there is a disabled when block that’s a literal port from the PDFBox annotation example, if you want to see how that syntax works.