Hello all, ### Environment: $ git --version git version 2.21.0 ### Reproduce: git clone git@xxxxxxxxxx: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