refactor(config): migrate from .env to YAML with OmegaConf

[looksaw2]

Migrated config storage from .env to config.yaml using OmegaConf.

• YAML replaces .env — all settings live in one config.yaml under llm / hugegraph
  / admin / index sections with nested structure.
• Hot reload — background file watcher picks up changes to config.yaml without
  restarting. Polling interval is configurable.
• Auto migration — existing .env is automatically converted to config.yaml on
  first run, no manual setup needed.
• Env vars take priority — OPENAI_API_KEY and similar secrets still come from
  environment variables, overriding YAML values (12-factor friendly).
• No breaking changes — llm_settings.language and all other attribute access works
  exactly the same, 46 consumer files untouched.

[imbajin]

Auto reviewed the config migration and found one blocking regression in environment-variable precedence.

[imbajin]

‼️ Preserve real environment-variable precedence

This loop copies every key from .env into os.environ before YAML/env override resolution. That reverses the intended deployment precedence when the process already has real environment variables: I reproduced this with .env containing OPENAI_API_KEY=from_dotenv while launching with OPENAI_API_KEY=from_real_env, and llm_settings.openai_chat_api_key became from_dotenv. Existing pydantic settings gave the real environment precedence over the dotenv file, so a stale local .env can override Docker/Kubernetes secrets after this migration. Please only fill missing keys from .env (for example os.environ.setdefault(...), skipping empty values) and add a regression test for env > .env/config.yaml precedence.

Suggested change

	os.environ[k] = v
	for k, v in dotenv_values(self._env_path).items():
	if v:
	os.environ.setdefault(k, v)