Add SUPPRESS_CONFIG_WARNINGS_STDERR AtomicBool flag in runtime/config.rs
and expose suppress_config_warnings_for_json_mode() via runtime crate.
In main.rs, scan raw argv for --output-format json before parse_args
and activate the flag so no settings-load warnings reach stderr on any
JSON-mode surface (status, sandbox, system-prompt, mcp list, skills list,
agents list, --resume /config*, etc.).
Text-mode surfaces are unaffected; prose deprecation warnings continue
to appear on stderr.
All 572+ tests pass (one pre-existing worker_boot failure unrelated).
de7edd5bb1