[BUG] Plan Mode can't be used with Bypass Permissions

Environment

• Platform (select one):
• [X ] Anthropic API (Claude Max)
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.72
• Operating System: macOS 15.5
• Terminal: iTerm2, tmux

Bug Description

Claude Code 1.0.72 accommodates --dangerously-skip-permissions by letting the user cycle between permissions, plan mode, and auto-accept edits with shift+tab. That new functionality means that Plan Mode cannot be used in conjunction with Bypass Permissions.

I use Bypass Permissions all the time during Plan Mode so Claude Code can run commands and use MCP tools to gather information about a problem. The smooth workflow is impeded by the fact that those states are now mutually exclusive.

Steps to Reproduce

1. Run claude --dangerously-skip-permissions
2. Activate Plan Mode with shift+tab
3. Ask Claude Code for a plan which involves a tool requiring permission, e.g. Playwright
4. Claude Code asks you for permission to invoke a tool even though you ran it with --dangerously-skip-permissions

Expected Behavior

claude --dangerously-skip-permissions turns on Bypass Permissions mode for the entire session, regardless of whether I'm in Plan Mode or not. Bypass Permissions should be first-class.

Actual Behavior

Bypass Permissions mode became a second-class mode, parallel to Plan Mode.