prep: remove deleted submodules from working tree

The directory of a submodule will be left behind in the git working tree when:

• The submodule has been removed from .gitmodules in the remote
• scap prep is run for a branch with an existing local checkout where the module still exists

This untracked submodule directories cause the apply-patches command to fail, as the working tree is not clean. This change makes sure we delete them after the local git checkout is updated

Bug: T359809