Unclear It is not stated how command-line allow rules and policy allow rules are merged.
What
Auto mode lets Claude act without asking you each time, using allow and deny rules set in autoMode. Allow rules used to be gathered from every settings source into one list.
They are now kept per source, and allow rules given on the command line (flagSettings) are merged with those from managed policy (policySettings, settings set by an administrator) before everything is combined.
Why
Managed policy may now limit allow rules passed on the command line.
Names in the bundleautoMode
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It is not stated how command-line allow rules and policy allow rules are merged.