An issue arises when we want to select individual --html-subjects including the root package, in that case a file named after the module name won't be created, but instead the index.html file will contain the data. Fixing this situation will introduce a breaking change for those using --html-subjects pointing to the root package: instead of the index.html they will end-up with the HTML file named by the root module name. Which makes more sens in my opinion, but it's still a breaking change (we could special-case the root module when it's selected in the html-subjects such that the index.html symlink will be created still, this would be the path of least resistance).
The workaround is to build the html pages inside a temporary directory and move/rename the selected subjects.