Copy provisioner cannot replace directory with symlink

I'm trying to play with the new image provisioner on our custom docker images, but one of layer failed to get copied, possibly due to a dangling symlink.

Error log with Glog_v=1:

I0324 05:42:48.926678 15067 copy.cpp:127] Copying layer path '/tmp/mesos/store/docker/layers/5df0888641196b88dcc1b97d04c74839f02a73b8a194a79e134426d6a8fcb0f1/rootfs' to rootfs '/var/lib/mesos/provisioner/containers/5f05be6c-c970-4539-aa64-fd0eef2ec7ae/backends/copy/rootfses/507173f3-e316-48a3-a96e-5fdea9ffe9f6'
E0324 05:42:49.028506 15062 slave.cpp:3773] Container '5f05be6c-c970-4539-aa64-fd0eef2ec7ae' for executor 'test' of framework 75932a89-1514-4011-bafe-beb6a208bb2d-0004 failed to start: Collect failed: Collect failed: Failed to copy layer: cp: cannot overwrite directory ‘/var/lib/mesos/provisioner/containers/5f05be6c-c970-4539-aa64-fd0eef2ec7ae/backends/copy/rootfses/507173f3-e316-48a3-a96e-5fdea9ffe9f6/etc/apt’ with non-directory

Content of /tmp/mesos/store/docker/layers/5df0888641196b88dcc1b97d04c74839f02a73b8a194a79e134426d6a8fcb0f1/rootfs/etc/apt points to a non-existing absolute path (cannot provide exact path but it's a result of us trying to mount apt keys into docker container at build time).

I believe what happened is that we executed a script at build time, which contains equivalent of:

rm -rf /etc/apt/* && ln -sf /build-mount-point/ /etc/apt