To give some initial context (excerpt from #535 (reply in thread)):

• Update of existing sites: That's for sure the most critical part. We do have two testimonies that users can upgrade to HEAD of repo and use their site successfully. In it's current form, there is some manual work needed. @LisaFC @chalin Is that acceptable? Yes or no? We need to make a decision here soon.
  That's what currently is needed to make the site work again:
  • navigate to your themes folder
  • create two new directory structures (empty directories):

  mkdir -p github.com/twbs/bootstrap
  mkdir -p github.com/FortAwesome/Font-Awesome
  

  No code change, simply create two empty directories and your site is up again. Is this acceptable? I don't see any good way to make it a seamless update without any intervention. I asked on the hugo discourse list, haven't received any answer yet. I doubt whether anyone will still come up with a good answer.
  Disclaimer: Yes, there actually is a way to make it a seamless update without any intervention. But it's not clean, and I don't like it.