In response to Mitsu's post about needing to see some dissertations that use hypertext. I searched the web and found some examples you all might be interested in exploring. Angel also did her Master's project in this manner, so you may be able to ask her to share her insights.
http://www.sympoiesis.net/?q=onlinediss#
(these are from the 90s, some links are broken, but provide are basic examples)
http://www.nutball.com/dissertation/mains/Narra1.html
(individual research)
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