Turned off Java binding in eXist's conf.xml file (in cocoon/WEB-INF), and the Java module continues to work fine, so we've nailed that.

Looking at the rendering of documents in my pilot install on Greg's machine, I noticed whitespace missing from mixed content. This is a problem we've encountered before, but it took a while to remember what needs doing. This part of conf.xml needs to be changed, from:

<indexer caseSensitive="yes" index-depth="5" preserve-whitespace-mixed-content="no" stemming="no" suppress-whitespace="both" tokenizer="org.exist.storage.analysis.SimpleTokenizer" track-term-freq="yes" validation="none">

to:

<indexer caseSensitive="yes" index-depth="5" preserve-whitespace-mixed-content="yes" stemming="no" suppress-whitespace="none" tokenizer="org.exist.storage.analysis.SimpleTokenizer" track-term-freq="yes" validation="none">

In other words, two changes to attribute values. Then you have to re-upload all the documents in the the db.