Quick update on this: Now if you remove a file locally (or from GIT in the case of CI/CD) and run "bundle deploy" from the CLI, it will remove the corresponding file from your Databricks workspace. 

e.g.
1. Add new file locally, run "bundle deploy"
2. File appears in Databricks workspace
3. Remove file locally, run "bundle deploy"
4. File is removed automatically from the Databricks workspace

Therefore, I don't think there's a need to manually do a cleanup of files.