text: Title: nb cli command changes the files without the pipeline.yaml
  Body: When running on the first pipeline example and running: !ploomber nb -f .ipynb
  The files will change from .py to ipynb but the pipeline would keep pointing to the .py files.
  
  This causes:
  1. The pipeline isn't functional.
  2. Users can revert back to the .ipynb files without changing the file manually.