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You need to pass in source filenames (rather than package names) with the javadoc command on the command line. (I don't know if this can be done in NetBeans)
"I have refined this fix to handle classes in unnamed packages. A link with the label <unnamed package> now appears at the top of the packge list when classes in unnamed packages are specified on the command line."
stddoclet: Include package info when passing in source filenames (*.java)
stddoclet: Want default (i.e. unnamed) package to appear in package list
11-Closed, duplicate of 4359386