Permission prompt appears despite --dangerously-skip-permissions flag

Bug Description

When running Claude Code with --dangerously-skip-permissions, the Edit tool still triggers a permission approval prompt. The prompt reappears for the same tool even after approving it once in the same session.

Reproduction Steps

1. Run claude --dangerously-skip-permissions
2. All three settings files confirm bypassPermissions:

• ~/.claude/settings.json — no permissions override
• .claude/settings.json — "defaultMode": "bypassPermissions" + allow: ["Read", "Write", "Edit", "Bash", "Glob", "Grep"]
• .claude/settings.local.json — "defaultMode": "bypassPermissions" + allow list

1. Ask Claude to edit a file (e.g., update a markdown file)
2. Expected: Edit executes without prompting
3. Actual: Permission approval popup appears for Edit / Update tool call

Additional Context

• The prompt reappears even after granting permission in the same session
• Platform: macOS (Darwin 24.6.0)
• No PermissionRequest hooks configured
• Plugins enabled: team-shinchan, slack, discord

Environment

• OS: macOS Darwin 24.6.0
• Shell: zsh