Follow up. I filed an issue
(http://www.netbeans.org/issues/show_bug.cgi?id=112921) with the Netbeans
development team regarding this. As it turns out, the extra jar files are in
the common/endorsed directory for backward compatibility with JDK 1.4 and
below. When Netbeans is used with a JDK newer than 1.4, the endorsed directory
is not being read, hence the error message that Xalan 2.7.0 can't be found.
Netbeans 6.0 comes with an unmodified Tomcat 6 meaning that there is no
undocumented or unexpected behavior like this to maintain any kind of backward
compatibility.
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