Today, [the logic](https://github.com/bazel-contrib/rules_bazel_integration_test/blob/dd36af23c4a7c8e97d91f22cc99504a19107c901/tools/create_scratch_dir.sh#L71) ignores hidden directories. We should copy over everything except `.git` and probably some other well-known source control directories.
