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This PR refactors EasyTier's configuration flags system across protobuf definitions, TOML/API persistence, runtime reconciliation, and the CLI. It introduces a synthesized FlagsPatch protobuf message with optionize and pbjson support to track field presence reliably, replaces manual CLI flag boilerplate with dynamic schema-driven clap argument generation, and establishes Flags::resolve(patch) as the single source of truth for runtime defaults. Co-authored-by: Claude Code <noreply@anthropic.com>