bug: Directory replaced by submodule -> checkout fails

Hello all,

### Environment:

$ git --version git version 2.21.0

### Reproduce:

git clone git@github.com:JuulLabs-OSS/mcuboot.git cd mcuboot git submodule init git submodule update git checkout ae01f153b11637feaedbc9d9042172fba2e080c0

### Discussion:

In the above sequence, the last step (checkout) fails with this error:

    error: The following untracked working tree files would be overwritten by checkout:
            ext/mbedtls/include/mbedtls/asn1.h
            ext/mbedtls/include/mbedtls/bignum.h
            ext/mbedtls/include/mbedtls/check_config.h
            ext/mbedtls/include/mbedtls/config.h
            ext/mbedtls/include/mbedtls/ecdsa.h
            ext/mbedtls/include/mbedtls/ecp.h
            ext/mbedtls/include/mbedtls/md.h
            ext/mbedtls/include/mbedtls/oid.h
            ext/mbedtls/include/mbedtls/pk.h
            ext/mbedtls/include/mbedtls/platform.h
            ext/mbedtls/include/mbedtls/platform_util.h
            ext/mbedtls/include/mbedtls/threading.h
    Please move or remove them before you switch branches.
    Aborting

In the mcuboot repo, a regular directory was recently replaced with a submodule. This was done with two separate commits:

1. (b748f6) Rename `ext/mbedtls` --> `ext/mbedtls-asn1`
2. (f984b9) Add submodule `ext/mbedtls`

Git reports an error when you use `git checkout` to "jump over" these two commits. The sequence above shows what happens when you go from post-replace to pre-replace (master to ae01f1).

When you do the reverse (pre-replace to post-replace), the checkout operation succeeds, but git emits the following warning:

    warning: unable to rmdir 'sim/mcuboot-sys/mbedtls': Directory not empty

This leaves the repo in a dirty state.

The problem is easy to work around by hand:

    rm -rf ext/mbedtls sim/mcuboot-sys/mbedtls
    git checkout ae01f153b11637feaedbc9d9042172fba2e080c0

Unfortunately it is not easy for automated tools to work around the issue.

Thanks, Chris