Bash tool prompts for permission on commands that should be auto-approved per settings

Bug Description

The Bash tool prompts the user for permission to run basic shell commands (ls, mkdir) even when the user's settings files (both ~/.claude/settings.json and .claude/settings.local.json) explicitly allow these commands.

Steps to Reproduce

1. Configure settings to allow basic shell commands (e.g., ls, mkdir) in ~/.claude/settings.json and/or .claude/settings.local.json
2. Ask Claude to perform a task that requires listing a directory or creating a directory via the Bash tool
3. Claude calls the Bash tool with e.g. ls /some/path or mkdir /some/path
4. The CLI prompts the user for permission instead of auto-approving

Expected Behavior

Commands explicitly allowed in settings files should be auto-approved without prompting the user.

Actual Behavior

The CLI prompts the user for approval. When the user rejects (because they shouldn't have been asked), the tool call fails.

Additional Context

• This has been observed across multiple sessions and conversations
• Affects at least ls and mkdir commands
• The user has confirmed the commands are present in their settings files as allowed