The eXist db now seems to require a full re-index whenever you upload files into it; they don't get properly indexed just through the upload process. My guess is that this is because we actually deployed a pre-release version, and there were some tweaks after it was fully released. My plan now is to build a new version with the Cocoon/eXist package I built on Monday for MJ, test that locally and then replace the server copy with it. I also want to make a further change to conf.xml, through my build script, as follows:

<db-connection cacheSize="48M" collectionCache="24M" database="native"
        files="webapp/WEB-INF/data" pageSize="4096" nodesBuffer="-1">

becomes

<db-connection cacheSize="48M" collectionCache="24M" database="native"
        files="webapp/WEB-INF/data" pageSize="4096" nodesBuffer="1000">

With the setting at -1, the system consumes all available memory when doing indexing; with it set to 1000, it keeps only 1000 nodes in memory at a time, leaving memory free for other threads.