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A removal asks the select for its empty choice and compared the result against that same empty choice, so applyOptions returned nothing and the manager stored the removal as null while the session ran the Default choice. The difference is now computed against what was asked (null), so the options hold the value the session runs with. The Codex plan-mode end-to-end tests called the removed session.setFeature through an optional call and silently skipped plan mode; they apply the option and fail loudly if the method is gone. The MCP parity wrapper forwards listControls instead of the removed listFeatures.