If gcj-jdk is used as java implementation, the generation of the HTML manual out of cp2k_input.xml fails like this:
Error on line 5 column 20 of cp2k_input.xml:
SXXP0003: Error reported by XML parser: malformed reference in entity value: "&"
Transformation failed: Run-time errors were reported
According to http://www.w3.org/TR/REC-xml/#sec-predefined-ent, the amp entry in a predefined entry section should be double-escaped, (the SourceForge website is apparently too clever, so I am leaving this out here, see the attached patch).
If I do this, the HTML is generated fine (note that the above link also says the lt entry should be escaped similarly, but at least in that Java XML implementation, this is not needed.