[BUG] --dangerously-skip-permissions ignores --permission-mode flag

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

Note: This issue was previously reported as a feature request in #11401, but it is actually a bug/regression in behavior.

What's Wrong?

When using --permission-mode plan --dangerously-skip-permissions together, the --dangerously-skip-permissions flag causes Claude to completely ignore the --permission-mode setting. Instead of starting in plan mode with permissions bypassed, it starts in bypass permissions mode.

The alternative flag --allow-dangerously-skip-permissions does respect the permission mode, but it prompts the user to trust the directory when launched. This is tedious and not what users expect when explicitly passing that flag.

What Should Happen?

• claude --permission-mode plan --dangerously-skip-permissions should start in plan mode with permissions bypassed (no prompts for read-only operations)
• The two flags should be composable: --permission-mode controls which mode to start in, --dangerously-skip-permissions controls whether to bypass permission prompts
• --allow-dangerously-skip-permissions should not prompt to trust the directory when used with an explicit --permission-mode

Steps to Reproduce

1. Run claude --permission-mode plan --dangerously-skip-permissions
2. Observe that Claude starts in bypass permissions mode, not plan mode
3. The --permission-mode plan flag is silently ignored

Alternative reproduction:

1. Run claude --permission-mode plan --allow-dangerously-skip-permissions
2. Claude prompts to trust the directory before starting
3. Previously this would drop directly into plan mode without prompting

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Unknown - but multiple users have confirmed this worked previously with --allow-dangerously-skip-permissions

Claude Code Version

2.1.4 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

See also: #11401 (mislabeled as feature request), #5466, #7136

Multiple users have confirmed this issue in #11401 and are actively requesting a fix.