Use yaml-reader to output GitHub workflows

[ArBridgeman]

Summary

In #667, we made the templates configurable with Jinja2 and validated the filled in YAML text with PyYaml.
To later do operations like replace/insert after in steps, it would be useful for us to use PyYaml's loading feature. PyYaml reads YAML files as a nested dictionary, but by default, it does not create YAMLs fully compatible with GitHub. In this PR, we adapt the default Dumper to preserve the necessary changes.