You can stop reading here if you don't care how I got this to work, or why I am a little bit surprised by this.
The Groovy-Eclipse plugin uses a feature patch on the JDT core bundle in order to achieve a high level of integration with JDT. Typically, feature patches can only apply to a specific version of a feature (e.g., 3.5.0.v20090527-2000-7r88FEeFJePyvYeA33DjZ_c1 or some ugliness). This means that Groovy-Eclipse, until recently could only install in a specific version of Eclipse, the one that ships the JDT feature version 3.5.0.v20090527-2000-7r88FEeFJePyvYeA33DjZ_c1. However, Andrew Niefer describes how to get around this by editing the content.xml file to widen the range that the patch applies to. Excellent stuff, and lucky for me, because I didn't want to branch the Groovy-Eclipse code base every time a new service release of Eclipse comes out.
Unfortunately, his instructions were not entirely accurate. Andrew mentions that the range attribute in the <patchscope> element needs to be widened in order allow the patch to be installable on multiple versions. I tried exactly what he suggested, but could not get my patch to install in both 3.5.0 and 3.5.1. After a little bit of exploration, I found that
All this meant was adding a single line to my ant script, to be executed after the p2 repository is generated:
And this turned out to be very simple. Thanks for the hint!