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[DOCS] Explicitly link --allowedTools CLI flags to permissions settings #18973
Description
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--allowedToolsCLI flag. - Key:
deny
Description: Array of permission rules to deny tool use. Corresponds to the--disallowedToolsCLI flag.
Impact
High - Prevents users from using a feature
Additional Context
Mapping clarification:
- CLI:
--allowedTools-> Settings:permissions.allow - CLI:
--disallowedTools-> Settings:permissions.deny
Activity
coygeek commentedon Jan 21, 2026
Thank you for the update to the documentation. I have reviewed the latest versions of the Settings and CLI Reference pages to see if the mapping between CLI flags and persistent configuration keys has been clarified.
What’s FIXED
--allowedToolsflag to the "permission rule syntax" section within the settings documentation. This improves navigation for users looking to understand how to format rules.What’s UNRESOLVED
allowanddenyfocus on functionality but do not inform the user that these are the persistent equivalents of--allowedToolsand--disallowedTools.~/.claude/settings.json. For a user trying to migrate a one-off command (e.g.,claude --allowedTools "Read") into a permanent project configuration, the documentation still requires them to infer thatpermissions.allowis the correct destination.Conclusion
I am keeping this issue open. While the documentation has improved with better internal linking, the specific request to update the "Permission settings" table with CLI flag equivalents has not been addressed. To fully resolve this, the table at https://code.claude.com/docs/en/settings#permission-settings should be updated so that:
allowkey description mentions it corresponds to--allowedTools.denykey description mentions it corresponds to--disallowedTools.github-actions commentedon Feb 27, 2026
Closing for now — inactive for too long. Please open a new issue if this is still relevant.
github-actions commentedon Mar 8, 2026
This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.