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Well, either treat your explanation as regular documentation and mention it in overview/package/class documentation (as appropriate) or simply add a link to your overview/package/class documentation that references the HTML file with your explanation. In the latter case, it should be possible to use a relative path since you can always copy the external HTML file into the directory structure created by javadoc. See http://docs.oracle.com/javase/1.5.0/docs/tooldocs/windows/javadoc.html#overviewcomment for information on overview comments and http://docs.oracle.com/javase/1.5.0/docs/tooldocs/windows/javadoc.html#packagecomment for information on package comments.
Thanks for the reply.
I was trying to get the javadoc tool to include the custom file in the generated output, but simply referencing it from the overview file and copying to the directory as you suggested makes perfect sense. I'll try it.