Don’t you just love obscure error messages?
rootNode.getElementsByTagName is not a function http://localhost:8080/js/dojo/dojo/geomajas-dojo.js.uncompressed.js Line 4674
After a couple of hours of debugging, checking all the differences etc, I figured out why the dojo application was no longer working.
I has assured all files have the corret copyright statement.
However, when dojo parses component templates, it seems to require a document with one root. So incluind the copyright at the top breaks everything. Oops.