Running diffs on before and after of javadoc output display inconsistent results, for clarity the diffs have been attached.

This particular case is in ModuleWriterImpl.java
     tdModules.addStyle(HtmlStyle.colSecond);
        List<? extends ModuleElement> targetModules = direct.getTargetModules();
        if (targetModules != null) {
            List<? extends ModuleElement> mElements = direct.getTargetModules();
            for (int i = 0; i < mElements.size(); i++) {
                if (i > 0) {
                    tdModules.addContent(new HtmlTree(HtmlTag.BR));
                }
                ModuleElement m = mElements.get(i);
                tdModules.addContent(new StringContent(m.getQualifiedName().toString()));
            }

The trouble in general is that the directives returned from a module descriptor is not deterministic. So this affects all these kinds of call sites. This must be fixed in either of two ways:
a. make the get*directive calls made to return consistent ordering
OR
b. introduce utility (Utils.java) methods which will return SortedSets and use these in all pertinent call sites.