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/filesystem.py

@@ -116,6 +116,25 @@ SEARCH_FILES_PARAMETERS: dict[str, Any] = {
     "required": ["query"],
 }
 
+WRITE_FILE_PARAMETERS: dict[str, Any] = {
+    "type": "object",
+    "properties": {
+        "path": {"type": "string", "description": "File path relative to the current workspace."},
+        "content": {"type": "string", "description": "Full file content to write."},
+    },
+    "required": ["path", "content"],
+}
+
+PATCH_FILE_PARAMETERS: dict[str, Any] = {
+    "type": "object",
+    "properties": {
+        "path": {"type": "string", "description": "File path relative to the current workspace."},
+        "old_text": {"type": "string", "description": "Exact text to replace."},
+        "new_text": {"type": "string", "description": "Replacement text."},
+    },
+    "required": ["path", "old_text", "new_text"],
+}
+
 
 class WorkspacePathError(ValueError):
     """Raised when a requested path escapes the configured workspace."""
@@ -158,6 +177,20 @@ def _resolve_existing_path(workspace: str | None, user_path: str | None) -> tupl
     return root, resolved
 
 
+def _resolve_writable_path(workspace: str | None, user_path: str | None) -> tuple[Path, Path]:
+    root = _workspace_root(workspace)
+    if not user_path or not str(user_path).strip():
+        raise WorkspacePathError("path is required")
+    raw_path = Path(str(user_path)).expanduser()
+    candidate = raw_path if raw_path.is_absolute() else root / raw_path
+    parent = candidate.parent.resolve(strict=True)
+    try:
+        parent.relative_to(root)
+    except ValueError as exc:
+        raise WorkspacePathError(f"path escapes workspace: {user_path}") from exc
+    return root, parent / candidate.name
+
+
 def _relative_path(root: Path, path: Path) -> str:
     try:
         return str(path.relative_to(root)) or "."
@@ -440,3 +473,73 @@ class SearchFilesTool:
             )
         except (OSError, WorkspacePathError, ValueError) as exc:
             return _json_result(False, error=str(exc), path=path)
+
+
+@dataclass(slots=True)
+class WriteFileTool:
+    """Write a UTF-8 text file inside the current workspace."""
+
+    name: str = "write_file"
+    description: str = (
+        "Write a UTF-8 text file inside the current workspace, replacing the full file. "
+        "Use patch_file for targeted edits. Paths outside the workspace are rejected."
+    )
+    toolset: str = "filesystem"
+    always_available: bool = False
+    workspace: str | None = None
+    parameters: dict[str, Any] = field(default_factory=lambda: dict(WRITE_FILE_PARAMETERS))
+
+    async def execute(self, *, path: str, content: str, workspace: str | None = None) -> str:
+        try:
+            root, resolved = _resolve_writable_path(workspace, path)
+            resolved.parent.mkdir(parents=True, exist_ok=True)
+            resolved.write_text(str(content), encoding="utf-8")
+            return _json_result(True, path=_relative_path(root, resolved), bytes=len(str(content).encode("utf-8")))
+        except (OSError, WorkspacePathError, ValueError) as exc:
+            return _json_result(False, error=str(exc), path=path)
+
+
+@dataclass(slots=True)
+class PatchFileTool:
+    """Replace an exact text fragment inside a workspace file."""
+
+    name: str = "patch_file"
+    description: str = (
+        "Replace an exact text fragment inside a UTF-8 workspace file. "
+        "Fails if old_text is missing or ambiguous."
+    )
+    toolset: str = "filesystem"
+    always_available: bool = False
+    workspace: str | None = None
+    parameters: dict[str, Any] = field(default_factory=lambda: dict(PATCH_FILE_PARAMETERS))
+
+    async def execute(
+        self,
+        *,
+        path: str,
+        old_text: str,
+        new_text: str,
+        workspace: str | None = None,
+    ) -> str:
+        try:
+            root, resolved = _resolve_existing_path(workspace, path)
+            if not resolved.is_file():
+                return _json_result(False, error="not_a_file", path=path)
+            content = _read_text_file(resolved)
+            occurrences = content.count(old_text)
+            if occurrences == 0:
+                return _json_result(False, error="old_text_not_found", path=path)
+            if occurrences > 1:
+                return _json_result(False, error="old_text_ambiguous", occurrences=occurrences, path=path)
+            updated = content.replace(old_text, new_text, 1)
+            resolved.write_text(updated, encoding="utf-8")
+            return _json_result(
+                True,
+                path=_relative_path(root, resolved),
+                old_bytes=len(old_text.encode("utf-8")),
+                new_bytes=len(new_text.encode("utf-8")),
+            )
+        except UnicodeDecodeError:
+            return _json_result(False, error="file is not valid UTF-8 text", path=path)
+        except (OSError, WorkspacePathError, ValueError) as exc:
+            return _json_result(False, error=str(exc), path=path)