refactor(agents): 删除 tools:agent:publish 命令，补全 helper.php 函数覆盖机制，修正多处文档 bug

- 删除 tools:agent:publish 整套（不再兼容多套 IDE，只保留 .agents 目录）
- helper.php 全部 27 个全局函数加 if (!function_exists()) 包裹，项目侧可在 app/common.php 定义同名函数覆盖
- ulthon-file-override-mechanism.md 新增全局函数覆盖章节
- AGENTS.md 删除智能体指导章节，PHP 8+ 改为 8.0+，MySQL 8+ 改为 5.7+
- AGENTS.md 项目结构树补全 tests/、extend/think/、source/ 子项
- README.md PHP 版本统一为 8.0+
- ulthon-base-app-architecture SKILL 路径补 admin/service/ 段
- ulthon-tools-http-call SKILL 补 --page-data 参数
- ulthon-naming-convention 补元数据头
- ulthon-update-workflow 统一 extend/think/ 归类

extend/think/UlthonAdminService.php

@@ -41,7 +41,6 @@ use app\common\command\tools\db\ToolsDbExecute;
 use app\common\command\tools\db\ToolsDbInfo;
 use app\common\command\tools\db\ToolsDbQuery;
 use app\common\command\tools\db\ToolsDbTable;
-use app\common\command\tools\agent\ToolsAgentPublish;
 use app\common\command\tools\log\ToolsLogSearch;
 use app\common\command\tools\log\ToolsLogShow;
 use app\common\command\tools\log\ToolsLogStats;
@@ -126,7 +125,6 @@ class UlthonAdminService extends Service
             Backup::class,
             ToolsHttpCall::class,
             MigrateFileData::class,
-            ToolsAgentPublish::class,
             ToolsDbQuery::class,
             ToolsDbExecute::class,
             ToolsDbTable::class,