EDIT: It looks like the problem might be caused by a failed transform of the conf.xml file near the end of the process. I need to look at that transformation and see why it's failing.

This morning I cleaned out the eXist tree and ran our build script with a fresh checkout. eXist seemed to build successfully, but I had a number of errors which had to be fixed before I could get the build of Cocoon to complete:

• Cocoon was finding a duplicate entry for commons-pool-1.5.4.jar in its jars.xml file. I don't know what is causing this, although the eXist build script now seems to be adding the second copy, so in my exist-jars_supplementary.xsl file, which post-processes the Cocoon jars.xml file, I put in a section to remove the second copy.
• The entry for ws-commons-util-1.0.2.jar was not being added into jars.xml. I think this was due to an error in the <xsl:if> clause that was checking for it in my exist-jars_supplementary.xsl, so I fixed that, and the error went away -- don't know why it worked last year.
• Cocoon complained about the presence of commons-pool-1.5.3.jar alongside 1.5.4. I don't know how that file makes it into the build, since eXist now uses 1.5.4, but I added a line to the script to delete it.
• The build now worked fine, and Cocoon comes up, but there are two problems we haven't seen before: the Cocoon samples page fails, and the eXist client dies with an error. Going to the admin page, I see an error with conf.xml. Replacing the conf file with a known good one does no good, so something is obviously screwy here. I have a help request up on the eXist list -- hopefully someone can tell me more about the error.

Spent most of my day on this, but I'm still not having any success. It appears that some patches were committed for some of the issues our script works around, but either they don't work properly, or there are new issues introduced by later changes. RvdB has been in touch, and is also interested in getting a working build, so I think we'll keep hacking at this.