feat(engine): 添加MCP连接管理和工具集成功能

- 集成MCP连接管理器，支持MCP服务器连接
- 添加多种内置工具：ClarifyTool、CronTool、DelegateTool、ExecuteCodeTool、
  PatchFileTool、ProcessTool、SendMessageTool、SpawnTool、TerminalTool、
  TodoTool、WebFetchTool、WebSearchTool、WriteFileTool等
- 实现工具注册和装配功能
- 添加技能选择上下文参数
- 支持思考模式控制参数thinking_enabled

feat(coordinator): 重构任务执行计划器参数命名

- 将learning_candidate_enabled重命名为allow_candidate_generation
- 更新TeamGraphScheduler中的参数传递
- 修改LocalAgentRunner中的相关参数处理
- 更新README文档中的相应描述

refactor(context): 标准化工具调用参数格式

- 添加_json导入用于参数序列化
- 实现_provider_tool_calls方法标准化OpenAI兼容的工具调用载荷
- 修复工具调用中参数非字符串类型的序列化问题

refactor(session): 优化消息历史记录过滤逻辑

- 修改get_messages_as_conversation为基于运行状态过滤消息
- 排除未完成、失败或错误结束的运行记录
- 改进对话历史的可见性控制机制

fix(store): 修复FTS索引重建逻辑

- 添加异常处理防止FTS索引创建失败
- 实现_rebuild_fts_index方法重新构建全文搜索索引
- 优化索引触发器和表的维护流程

app-instance/backend/beaver/tools/builtins/__init__.py

@@ -1,19 +1,39 @@
 """Built-in Beaver tools."""
 
+from .cron import CronTool
 from .echo import EchoTool, echo_tool
-from .filesystem import ListDirectoryTool, ReadFileTool, SearchFilesTool
+from .filesystem import ListDirectoryTool, PatchFileTool, ReadFileTool, SearchFilesTool, WriteFileTool
 from .memory import MemoryTool, memory_tool
+from .skills_admin import SkillManageTool, SkillsListTool
 from .skill_view import SkillViewTool, skill_view
 from .session_search import SessionSearchTool, session_search
+from .terminal import ExecuteCodeTool, ProcessTool, TerminalTool
+from .utility import ClarifyTool, DelegateTool, SendMessageTool, SpawnTool, TodoTool
+from .web import WebFetchTool, WebSearchTool
 
 __all__ = [
     "EchoTool",
+    "ExecuteCodeTool",
+    "CronTool",
+    "DelegateTool",
     "ListDirectoryTool",
     "MemoryTool",
+    "PatchFileTool",
+    "ProcessTool",
     "ReadFileTool",
     "SearchFilesTool",
+    "SendMessageTool",
+    "SpawnTool",
+    "SkillManageTool",
+    "SkillsListTool",
     "SkillViewTool",
     "SessionSearchTool",
+    "TerminalTool",
+    "TodoTool",
+    "ClarifyTool",
+    "WebFetchTool",
+    "WebSearchTool",
+    "WriteFileTool",
     "echo_tool",
     "memory_tool",
     "skill_view",