The only pages that link to overview-tree.html when I run this is the root and the USE pages. The regular class documentation links to the package-tree.html files for me.
javadoc {packages|source-files} [options] [@argfiles]
I believe the issue here is that Javadoc’s behavior subtly changes depending on whether packages or source-files are given. I’m not aware of any reason that this would be the desired behavior of javadoc, but I’m not sure you can fix it without calling javadoc differently. I believe the methods mentioned in this post from earlier in the year would help you achieve this, if it’s a deal breaker.