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thinkingLevels was excluded from the mergeDefaults whitelist in PreferencesManager, so user choices were silently dropped on every save/load cycle and never written to preferences.json. Add the field to the Preferences interface, DEFAULTS, and mergeDefaults so the existing backendPersist → savePreferences pipeline can write and restore it correctly. Adds regression tests covering the save/load round-trip, multi-save merge, and legacy-file backward compatibility. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>