What
Allow rules let a tool run without asking you first. At startup, Claude Code now checks each entry you pass with --allowedTools and each entry in the permissions.allow setting. If an entry matches a rule that Claude Code always allows anyway, you get a warning, shown both as an ordinary warning and as a security warning.
Why
You may start seeing these warnings for allow rules that have no effect, and can remove those rules.
Names in the bundlepermissions.allow
Documented inclaude-code/admin-setup
permissions.allow
Claude apps gateway configuration modified, high confidence
> Policies can add up to looser rules than any one of them gives alone. For example, the `match: {}` policy sets `sandbox.enabled: true`, one group's policy sets `permissions.allow: ["Bash"]`, and another group's sets `sandbox.enabled: fal…see the edit
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Anthropic's documentation agrees
permissions.allow on Claude apps gateway configuration