Late last year I contacted this company Qoppa Software
with a similar idea.
Their PDF Studio
has all the capabilities (and more) that everyone seems to want available in a linux package. They have an Android app qPDFnotes
as well that does pretty much what is wanted for the Onyx reader .
Basically they would be willing to port a version for a reader if there was enough community interest. They have all the necessary linux tools/libraries to do it .
My contact there was
+1 (404) 685-8733
in my opinion this would be a much better solution than an xjournal port if its actually doable.
thre is a video of the android app in operation http://www.youtube.com/watch?v=Of1rT4i0F_Q