libgit2 breaks when merging a submodule change into a branch where that submodule has been deleted

[x.zip](https://github.com/twosigma/git-meta/files/1519629/x.zip)
Using the attached zip or this:
```bash
$ write-repos -o 'a=B:Ca-1;Ba=a|x=U:C3-2 s;C5-4 foo=bar;C4-2 s=Sa:a;Bmaster=3;Bfoo=5'
```
Do the following to reproduce:
```bash
$ cd x
$ git meta merge -m foo foo
Error: object not found - no match for id (64ba9179dc7865187060226f21f4f7642ac783a1)
```

The relevant lines are:

```JavaScript
const mergeIndex = yield SubmoduleUtil.cacheSubmodules(repo, () => {
return NodeGit.Merge.commits(repo, head, commit, null);
});

const checkoutOpts = {
checkoutStrategy: NodeGit.Checkout.STRATEGY.FORCE
};
yield SubmoduleUtil.cacheSubmodules(repo, () => {
return NodeGit.Checkout.index(repo, mergeIndex, checkoutOpts);
});
```

And it is the attempt to checkout the merge index where it dies.