Run command rewrites config.xml

While other command are expected to alter `config.xml`, `run` is not a command I would expect to change it.
When I edit `config.xml` to make the xml consistent or pretty I don't expect `run` to rewrite it.

Start with the run command's handling of config.xml and reproduce the issue by formatting the file before invoking run. Trace where run writes the configuration, then verify that running the command preserves the file's formatting while other commands retain their expected behavior.

Written by the indexing model from the issue text.