[BUG] Thinking mode setting in settings.json not persisted across sessions

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

The alwaysThinkingEnabled: false setting in ~/.claude/settings.json does not persist across sessions. Thinking mode resets to true on every new session, requiring manual toggle via /config each time.

What Should Happen?

The alwaysThinkingEnabled setting should be respected on session start. If set to false, thinking mode should remain off without requiring manual intervention.

Error Messages/Logs

N/A

Steps to Reproduce

1. Set {"alwaysThinkingEnabled": false} in ~/.claude/settings.json
2. Start a new Claude Code session
3. Run /config and observe that Thinking mode shows true instead of false

Claude Model

Opus

Is this a regression?

Unknown

Last Working Version

_No response_

Claude Code Version

2.0.67

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Related to #13759 - both issues concern thinking mode toggle UX. A keyboard shortcut to toggle thinking mode would also help as a workaround.