Doctr fails if not run in the root directory of the repo

[asmeurer]

See for instance https://travis-ci.org/asmeurer/iterm2-tools/jobs/298968310, where it can't create .nojekyll because it's in a directory that no longer exists after the stash. Possibly other things could fail as well (e.g., the encryption key is put in the main directory first).

We should check if the directory we are in exists after checking out the deploy branch, and check for other potential issues here as well (and if we change dirs, we need to modify --built-docs so that it's still correct relative to where we were).