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Use entry metadata to discover registration evidence independently of target readability. Preserve failed metadata inspection as a named invalid diagnostic instead of treating all lookup failures as absence. Remove the duplicate boolean existence wrapper; configuration parsing remains the read owner. Cover native permission-denied targets and metadata, dangling configuration entries, maintenance exclusion, and public doctor output without mutation. Validation: 73 focused tests across four files, check:fast, format:check, and six isolated completed public doctor cost comparisons passed on macOS arm64 / Node24.18.0. Native Windows/Linux permissions were not verified; POSIX permission controls skip unsupported hosts and root. Fixes #4905