[BUG] --dangerously-skip-permissions does not bypass runtime tool execution prompts

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?

--dangerously-skip-permissions does not suppress tool execution prompts during a session.
Even trivial Bash commands like claude --version prompt for user confirmation,
indicating bypass mode is not active for runtime tool calls.

The startup dialog IS correctly suppressed (via skipDangerousModePermissionPrompt: true
in ~/.claude/settings.json), so the flag is partially recognized — but it has
no effect on actual tool execution permissions. Behavior is identical to normal
permission mode with an allow/deny list, as if the flag were ignored entirely.

What Should Happen?

In bypass permissions mode, zero tool execution prompts should appear.
All Bash commands, Write, Edit, and other tools should execute immediately
without confirmation, regardless of the allow/deny lists in settings.json.

Error Messages/Logs:
Bash command
claude --version 2>/dev/null || echo "version check failed"
Check Claude Code version

Do you want to proceed?
> 1. Yes

1. Yes, and don't ask again for: claude --version
2. No

Error Messages/Logs

Steps to Reproduce

1. Ensure ~/.claude/settings.json contains:

```json
{
"skipDangerousModePermissionPrompt": true,
"permissions": {
"allow": ["Bash(wc:*)"],
"deny": []
}
}

1. Launch Claude Code:

claude --verbose --dangerously-skip-permissions --model claude-opus-4-6

1. Ask Claude to run any Bash command NOT in the allow list, e.g.:

claude --version

1. Permission prompt appears instead of executing immediately.

Note: The --verbose flag precedes --dangerously-skip-permissions.
Untested whether reordering flags changes the behavior.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

N/A

Claude Code Version

2.1.86 (Claude Code)

Platform

Other

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

Relation to #25503

#25503 covers the startup dialog not being bypassed by the flag alone.
This issue is distinct: the flag fails to bypass runtime tool execution
prompts entirely.

Possible Cause

• Flag ordering: --verbose precedes --dangerously-skip-permissions

and may interfere with flag parsing.

• The permissions.allow/permissions.deny lists in settings.json may

override or take precedence over the bypass flag, when they should be
completely ignored in bypass mode.