file endings from yml to yaml

[garland3]

rename config files from yml to yaml.
accept both for now

[garland3]

Does this cover just the app config under atlas/config/ (e.g. llmconfig.yml and the LLM_CONFIG_FILE default), or repo-wide including docker-compose.yml and the .github/workflows/*.yml files? And when both foo.yaml and foo.yml are present, should .yaml win silently or log a deprecation warning for the .yml one?

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