Add Hermes Agent init support

[nathanBurg]

Summary

• add Hermes Agent to init detection and setup using hermes-agent plus ~/.hermes/HERMES_HOME
• add YAML config-file support for Hermes mcp_servers while preserving comments and handling null sections
• document Hermes Agent support and cover setup/uninstall/check paths with tests

Verification

• bun run typecheck
• bun run format:check
• bun test
• bun run build
• bun run lint
• bun run smoke:cli (skipped with AUTH_REQUIRED)