There is this tool called cabal-prettify that I built some time ago. I just put online a new version that will add whatever modules it can find to exposed-modules or other-modules automagically, so long as you give it the flag expose.
cabal-prettify can also enforce neat folder layout, with the flag move.
If you wish to try it out, you can get an executable built by the integration script on GitHub, or you can clone and build from source. I have not put it on Hackage yet.
Let me know if you find it handy!