My paper from the Cologne colloquium has been published in:
Historical and Social Research / Historische Sozialforschung 37.3 (2012), 125-146.
It contains a fairly detailed description of my alternative to embedded XML markup as an overall system for representing texts in the digital humanities, and how interoperable software can be built upon that foundation. Since it is a subscription-only journal I can't publish the text here, but a free copy of that volume is reportedly being given to all attendees to the current Digital Humanities conference at Hamburg this year. So it should be read by a wide audience.