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Fixed an issue where extraneous and inaccurate debug logs were added when parsing yaml files
Fixed an issue where the nest command threw an error when manifests were already nested. The nest command now just copies already nested directories to the output dir
Fixed an issue where the flatten command threw an error when manifests were already flattened. The flatten command now just copies already flattened directories to the output dir
Fixed an issue where nest and flatten were not ignoring files unrelated to the manifests in directories or subdirectories