The next version of the app will handle that beautifully.
The problem right now is that the only way to mark an upload as "html" is to make it "Playable in the browser" (and thus, free). So technically the site isn't set up to let you sell HTML games. But in the next version, the app will treat games as "probably native, but also potentially HTML" so if it doesn't find any native executables and it finds an index.html, it'll treat it as an HTML game. No need for a manifest.
Until then.. sorry for the trouble :(