Hi,
There's something which I have thought about more than once, even if it is a trivial detail. I have a done a lot of dub inits for little tools, so I have a lot of app.d files in my system. If I want to quickly open one of them (using Spotlight or a similar quick search service) I can't directly search for the one and only D source file for that project, because there are too many app.d files for the search results to be useful. Have you considered naming the initial file the same as the new package? E.g. dub init foobar would create source/foobar.d.
Regards,
Luís