Whenever Dyad does a commit from a proposal, it will automatically amend
the commit with outside changes (e.g. made outside of Dyad).

This helps avoid a lot of user confusion, e.g.
https://github.com/dyad-sh/dyad/issues/187

https://www.reddit.com/r/dyadbuilders/comments/1kjysc0/error_pushing_images/

Edge cases:
If a user adds a file outside of Dyad, and then they hit retry, it will
revert these outside changes, but it's still technically in the version
history, so I think it's OK. This should also be a pretty unusual
situation.

Fixes #164 
Fixes #187