Pull example doesn't fully update the index

@ubercow

Following the pull example and doing a simple fast-forward pull you'll get the inverse of what was changed in your working directory.

Repo Steps

Doing a nodegit.Checkout.head doesn't update the index either.

Originally reported by @ubercow

We should rebase this branch on master now to see if it still performs the same way.

Doing

var opts = { checkoutStrategy: nodegit.Checkout.STRATEGY.FORCE };
return nodegit.Checkout.head(repo, opts);

after mergeBranches updates the index.
Obviously this might result in losing stuff.
For some reason STRATEGY.SAFE doesn't seem to cut it.

Relevant references:

That example is almost 2 years old and has been updated since then as the API has changed.

This was updated in #505