refactor(config): preserve explicit flags with FlagsPatch and derive CLI arguments from schema (#2585)

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>

easytier-web/frontend-lib/scripts/codegen-proto.mjs

@@ -15,6 +15,7 @@ const protocWrapper = require.resolve('@protobuf-ts/protoc/protoc.js')
 const protobufTsPluginRoot = dirname(require.resolve('@protobuf-ts/plugin/package.json'))
 
 const protoFiles = [
+  'annotations.proto',
   'common.proto',
   'acl.proto',
   'api_instance.proto',