This morning I did a checkout (without deleting the existing tree) and a build; the JNLP link failed, and required that the cocoon app directory be inserted into it to get a working link. However, immediately afterwards I deleted the source tree and did a fresh checkout, and it worked correctly. It's clear that the file controller-config.xml is nothing to do with the problem, because that file is identical in the broken and working versions. It seems that deleting the source tree solves the problem. Now we need to see whether a simple build clean will solve it. More experiments continuing.