[Bug] acceptEdits defaultMode not persisted; Write permissions reset after first file operation

Bug Description
Title: acceptEdits + Write in permissions.allow not honored; file writes still prompt Environment: Claude Code v2.1.162 (native), macOS (Apple Silicon), Ghostty, Claude Max, Opus 4.8. Issue: With defaultMode: acceptEdits and Read/Edit/Write explicitly in permissions.allow (in both ~/.claude/settings.json and project .claude/settings.local.json), file writes still trigger permission prompts. /permissions confirms Write is in the Allow list, yet it prompts anyway. Key symptom: The first file write in a session is auto-approved silently, but the next identical write prompts with the default-mode dialog. Two identical operations get different treatment in one session, suggesting the permission mode resets at runtime instead of staying on acceptEdits. Repro: Set defaultMode: acceptEdits + allow: ["Read","Edit","Write"]. Launch claude from the project root. Ask it to create one file (writes silently), then a second file (prompts). Ruled out: valid JSON (both files), Write confirmed in Allow via /permissions, not Full Disk Access (first write succeeds), all plugins disabled, Ghostty fully restarted. Only bypassPermissions stops the prompts. Expected: With acceptEdits and Write allowed, in-project writes should never prompt.

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.1.162
• Feedback ID: 4e4dd27f-ba37-4f26-83c9-adf714fb0948

Errors

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