[DOCS] Explicitly link `--allowedTools` CLI flags to `permissions` settings

Documentation Type

Missing documentation (feature not documented)

Documentation Location

• https://code.claude.com/docs/en/settings#permission-settings - https://code.claude.com/docs/en/cli-reference

Section/Topic

The "Permission settings" table in the Settings documentation.

Current Documentation

In settings.md, the table lists:

• allow: "Array of permission rules to allow tool use. Note: Bash rules use prefix matching, not regex"
• deny: "Array of permission rules to deny tool use..."

Separately, in cli-reference.md, the documentation lists:

• --allowedTools: "Tools that execute without prompting for permission..."
• --disallowedTools: "Tools that are removed from the model's context..."

What's Wrong or Missing?

The documentation does not explicitly link these two configuration methods. A user familiar with the --allowedTools CLI flag who wants to make that configuration persistent in settings.json might not immediately realize that permissions.allow is the direct equivalent. The mapping between the CLI flags and the JSON configuration keys is implied but not stated.

Suggested Improvement

In the Permission settings table on the Settings page (https://code.claude.com/docs/en/settings#permission-settings), update the descriptions to reference the CLI equivalents:

• Key: allow

Description: Array of permission rules to allow tool use. Corresponds to the --allowedTools CLI flag.

• Key: deny

Description: Array of permission rules to deny tool use. Corresponds to the --disallowedTools CLI flag.

Impact

High - Prevents users from using a feature

Additional Context

Mapping clarification:

• CLI: --allowedTools -> Settings: permissions.allow
• CLI: --disallowedTools -> Settings: permissions.deny