Proposal: Suppress config.toml deprecation warnings when legacy keys originate from Cloud-Managed/Enterprise layers (Fix for #53293)

[yhpop]

Overview & Proposal

As reported in Issue #53293 (#53293), users in Enterprise / Team organizations currently encounter un-dismissible deprecation callout banners in the ChatGPT macOS App (Settings -> Configuration):

[features.guardianv2].thread_context is deprecated and ignored.
Thread-owned Guardian context is always enabled. Remove thread_context from [features.guardianv2] in config.toml, including profile overrides.

Because the key is injected by the OpenAI backend workspace bundle (enterpriseManaged layer) and does not exist in any local file, the user cannot edit or remove it.

Proposed Architectural Improvements

1. Source-Aware Deprecation Dispatcher in codex-features:
   In Features::from_sources, check the ConfigSource variant. Only push to legacy_notices when the layer is User, Project, or Profile. Silently ignore or downgrade to internal debug logs for EnterpriseManaged, System, or PackagedDefaults.
2. Graceful Handling of Permanently Enabled Defaults:
   For legacy flags like guardianv2.thread_context whose behavior is now permanently active in core runtime, avoid recording legacy notices on automated/cloud layers.
3. Frontend Guard in configuration-panel.js:
   Filter out callouts when isManagedScopeActive is true and !notice.path.
4. Backend Template Maintenance:
   Scrub retired flags from baseline workspace configuration bundles.

Full reverse-engineering analysis and assembly proofs are documented in Issue #53293. We welcome the team to adopt this refinement in the next desktop & CLI release!

[yhpop]

Gist with Unified Diff Patch & Technical Architecture Documentation: https://gist.github.com/yhpop/1d622659e4667c566ad82a11ae89ef1d