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prep: remove deleted submodules from working tree

Jaime Nuche requested to merge T359809 into master

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

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