In thinking about how Xournal can be integrated into other tools, I think the following could be very useful:
1) A way of extracting out of an xoj file all text annotations, and their respective locations, both as page-numbers and (possibly) some more specific location designator that can be given to xournal to jump directly to this location / highlight the element, etc. Maybe this could just be some commandline option like '--list-annotations' that can be given to xournal with a particular xoj file.
2) A commandline option (e.g. --jumpto <location-id>) which causes xournal to jump to (and maybe highlight) a specific location. If the filename given to xournal is open in an already-running xournal instance, then another option (e.g. --singleinstance) can be used to force the existing instance to scroll to / highlight the specified location.
If these two items were implemented, it would make Xournal much easier to integrate into PDF / reference-management (and other) software. For example, the ref-mgmt software could, for any of the PDFs it is managing, list all of the text annotations, and their respective locations in the PDF. Furthermore, any of these text annotations could be (for example) double-clicked on to launch xournal with the annotation highlighted/selected. I can see that being very useful.