astro dbt cleanup only removes .astro/dbt_metadata.json and .astro/manifest.slim.json files that the Cosmos Boost pre-deploy step generated. It doesn’t remove any other files under .astro/.
astro dbt
astro dbt cleanup
Remove Cosmos Boost pre-deploy artifacts from a dbt project.
Remove Cosmos Boost artifacts from one or more paths in your local project. Use this command after you disable the Cosmos Boost pre-deploy step, or to clear artifacts left by an earlier deploy.
To remove Cosmos Boost artifacts from specific paths: