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Following steps are taken: git submodule deinit -f -- a/submodule git submodule deinit -f -- a/srm -rf .git/modules/a/submodule rmdir a/submodule fails because git still holds this empty sm directory, we can't remove it. side effect: you can't install -> uninstall -> install the same extension
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fixes (partially): #466 (check issue for details)