--dangerously-skip-permissions no longer skips permissions listed in managed-settings.json

Description

--dangerously-skip-permissions flag no longer skips permission prompts for tools listed under the deny or managed permissions in managed-settings.json. This is a behavior change introduced in a recent version.

Expected Behavior

When running Claude Code with --dangerously-skip-permissions, all permission checks should be bypassed, including those enforced via managed-settings.json. The flag name itself implies that it should skip all permissions dangerously.

Actual Behavior

Permissions defined in managed-settings.json are still enforced even when --dangerously-skip-permissions is passed. The flag only appears to skip interactive prompts for tools not covered by managed settings, but does not bypass the managed policy restrictions.

Steps to Reproduce

1. Add a tool to the deny list (or configure restrictions) in managed-settings.json
2. Run Claude Code with --dangerously-skip-permissions
3. Observe that the tool is still blocked despite the flag

Environment

• Claude Code version: 2.1.168
• OS: macOS (Darwin 25.5.0)

Additional Context

This appears to be a regression — prior behavior was that --dangerously-skip-permissions would bypass all permission checks including managed settings. Not sure in which version this behavior changed.

This is particularly impactful for automated/CI use cases where --dangerously-skip-permissions is used to run non-interactively, but managed-settings.json policies (e.g. set by an organization) inadvertently block tools needed for the automation.