docs: discourage MCP filesystem workspace config (#3141)

frontend/src/content/en/harness/mcp.mdx

@@ -29,11 +29,6 @@ The default location is the project root (same directory as `config.yaml`). The
       "args": ["-y", "@my-org/my-mcp-server"],
       "enabled": true
     },
-    "filesystem": {
-      "command": "npx",
-      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/dir"],
-      "enabled": true
-    },
     "sqlite": {
       "command": "uvx",
       "args": ["mcp-server-sqlite", "--db-path", "/path/to/db.sqlite"],
@@ -43,6 +38,16 @@ The default location is the project root (same directory as `config.yaml`). The
 }
 ```
 
+<Callout type="warning">
+  Do not add an MCP filesystem server for DeerFlow workspace files. DeerFlow
+  already provides built-in file tools for thread-scoped workspace access, and
+  overlapping file tools with different path semantics can make LLM tool
+  selection and file access behavior unstable. DeerFlow does not currently
+  adapt MCP Roots mode for filesystem servers: it does not publish per-thread
+  MCP roots or map sandbox paths such as <code>/mnt/user-data/...</code> to
+  paths accepted by <code>@modelcontextprotocol/server-filesystem</code>.
+</Callout>
+
 Each server entry supports:
 
 - `command`: the executable to run (e.g., `npx`, `uvx`, `python`)

frontend/src/content/zh/application/configuration.mdx

@@ -193,15 +193,23 @@ BETTER_AUTH_SECRET=local-dev-secret-at-least-32-chars
 ```json
 {
   "mcpServers": {
-    "filesystem": {
+    "my-server": {
       "command": "npx",
-      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/dir"],
+      "args": ["-y", "@my-org/my-mcp-server"],
       "enabled": true
     }
   }
 }
 ```
 
+<Callout type="warning">
+  不要为 DeerFlow 工作区文件引入 MCP filesystem server。它会与 DeerFlow
+  内置文件工具形成路径语义不同的重复能力，让 LLM 行为不稳定。DeerFlow
+  当前没有为 filesystem server 适配 MCP Roots 模式，也不会把{" "}
+  <code>/mnt/user-data/...</code> 这类沙箱路径映射成{" "}
+  <code>@modelcontextprotocol/server-filesystem</code> 可接受的路径。
+</Callout>
+
 ### 技能启用状态
 
 技能启用状态会反映在 `extensions_config.json` 中。你可以直接编辑它，或通过 DeerFlow 应用界面进行管理。

frontend/src/content/zh/harness/mcp.mdx

@@ -28,11 +28,6 @@ MCP 服务器在 `extensions_config.json` 中配置，这个文件独立于 `con
       "args": ["-y", "@my-org/my-mcp-server"],
       "enabled": true
     },
-    "filesystem": {
-      "command": "npx",
-      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/dir"],
-      "enabled": true
-    },
     "sqlite": {
       "command": "uvx",
       "args": ["mcp-server-sqlite", "--db-path", "/path/to/db.sqlite"],
@@ -42,6 +37,15 @@ MCP 服务器在 `extensions_config.json` 中配置，这个文件独立于 `con
 }
 ```
 
+<Callout type="warning">
+  不要为 DeerFlow 工作区文件引入 MCP filesystem server。DeerFlow 已提供按
+  thread 隔离的内置文件工具；重复引入路径语义不同的文件工具，会让 LLM
+  的工具选择和文件访问行为不稳定。DeerFlow 当前没有为 filesystem server
+  适配 MCP Roots 模式：不会发布按 thread 收窄的 MCP roots，也不会把{" "}
+  <code>/mnt/user-data/...</code> 这类沙箱路径映射成{" "}
+  <code>@modelcontextprotocol/server-filesystem</code> 可接受的路径。
+</Callout>
+
 每个服务器条目支持：
 
 - `command`：要运行的可执行文件（如 `npx`、`uvx`、`python`）