After giving a demo of my online PDF annotation assignment plugins to Martin D during the Dublin Moodle Moot he was very keen that these should become part of core in Moodle 2.5.
The current code can be found here:
https://github.com/davosmith/moodle-assignsubmission_pdf
https://github.com/davosmith/moodle-assignfeedback_pdf

There are a number of issues I can see with this (all of which have, so far, been answered with a 'we can tidy them up later'):

• This is a Moodle 1.9 assignment type, converted to a Moodle 2.0 assignment type, converted to a pair of Moodle 2.3 assign plugins (feedback / submission), that has developed far more than ever originally intended => the code (especially the javascript) is a bit messy in many places.
• The main javascript library is Mootools (this seemed like a good idea 4 years ago when I started)
• The tools buttons are YUI2 code
• There is a requirement for ghostscript to be installed on the server (which would need some extra code to check for this and disable the plugin if ghostscript was unavailable)
• There are no unit tests

On the positive side:

• It works (although the code has been tested more thoroughly in the mod_assignment version, as it has only recently been converted to Moodle 2.3+)
• It has a good range of tools that are useful to a teacher annotating assignments (as I spent about 3 years using it to mark assignments, as I developed it).
• Apart from the ghostscript requirement, the only other requirement is the FPDI library which is PHP code and licensed under the Apache License v2.0 (this needs one, very small, modification to work properly within Moodle)