feat: 重构配置布局，server.listen/storage/logging + probes.execution 分组

- 新增 server.listen (host/port)、server.storage (dataDir/retention)、
  server.logging 分组
- 新增 probes.execution (maxConcurrentChecks) 分组，替代顶层 runtime
- 旧配置入口 (runtime/logging/server.host/server.port/server.dataDir)
  启动期拒绝
- 更新 types.ts、builder.ts、config-loader.ts 适配新路径
- 更新 probe-config.schema.json、probes.example.yaml、README.md、
  DEVELOPMENT.md
- 补充 config-loader 和 variables 测试覆盖新路径和旧入口拒绝
- 同步 5 个 delta specs 到主规范 (probe-config, config-variables,
  data-retention, probe-engine, runtime-logging)
- 归档 openspec change reorganize-config-layout

probes.example.yaml

@@ -1,24 +1,26 @@
 # yaml-language-server: $schema=./probe-config.schema.json
 
 server:
-  host: "127.0.0.1"
-  port: 3000
-  dataDir: "/tmp/probes_data"
+  listen:
+    host: "127.0.0.1"
+    port: 3000
+  storage:
+    dataDir: "/tmp/probes_data"
+  # logging:
+  #   level: "info"
+  #   console:
+  #     level: "info"
+  #   file:
+  #     level: "info"
+  #     path: "/var/log/dial/dial.log"
+  #     rotation:
+  #       size: "50MB"
+  #       frequency: "daily"
+  #       maxFiles: 14
 
-runtime:
-  maxConcurrentChecks: 20
-
-# logging:
-#   level: "info"
-#   console:
-#     level: "info"
-#   file:
-#     level: "info"
-#     path: "/var/log/dial/dial.log"
-#     rotation:
-#       size: "50MB"
-#       frequency: "daily"
-#       maxFiles: 14
+probes:
+  execution:
+    maxConcurrentChecks: 20
 
 defaults:
   interval: "30s"