feat: implement file upload feature

backend/docs/FILE_UPLOAD.md

@@ -0,0 +1,287 @@
+# 文件上传功能
+
+## 概述
+
+DeerFlow 后端提供了完整的文件上传功能，支持多文件上传，并自动将 Office 文档和 PDF 转换为 Markdown 格式。
+
+## 功能特性
+
+- ✅ 支持多文件同时上传
+- ✅ 自动转换文档为 Markdown（PDF、PPT、Excel、Word）
+- ✅ 文件存储在线程隔离的目录中
+- ✅ Agent 自动感知已上传的文件
+- ✅ 支持文件列表查询和删除
+
+## API 端点
+
+### 1. 上传文件
+```
+POST /api/threads/{thread_id}/uploads
+```
+
+**请求体：** `multipart/form-data`
+- `files`: 一个或多个文件
+
+**响应：**
+```json
+{
+  "success": true,
+  "files": [
+    {
+      "filename": "document.pdf",
+      "size": 1234567,
+      "path": ".deer-flow/threads/{thread_id}/user-data/uploads/document.pdf",
+      "virtual_path": "/mnt/user-data/uploads/document.pdf",
+      "artifact_url": "/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/document.pdf",
+      "markdown_file": "document.md",
+      "markdown_path": ".deer-flow/threads/{thread_id}/user-data/uploads/document.md",
+      "markdown_virtual_path": "/mnt/user-data/uploads/document.md",
+      "markdown_artifact_url": "/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/document.md"
+    }
+  ],
+  "message": "Successfully uploaded 1 file(s)"
+}
+```
+
+**路径说明：**
+- `path`: 实际文件系统路径（相对于 `backend/` 目录）
+- `virtual_path`: Agent 在沙箱中使用的虚拟路径
+- `artifact_url`: 前端通过 HTTP 访问文件的 URL
+
+### 2. 列出已上传文件
+```
+GET /api/threads/{thread_id}/uploads/list
+```
+
+**响应：**
+```json
+{
+  "files": [
+    {
+      "filename": "document.pdf",
+      "size": 1234567,
+      "path": ".deer-flow/threads/{thread_id}/user-data/uploads/document.pdf",
+      "virtual_path": "/mnt/user-data/uploads/document.pdf",
+      "artifact_url": "/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/document.pdf",
+      "extension": ".pdf",
+      "modified": 1705997600.0
+    }
+  ],
+  "count": 1
+}
+```
+
+### 3. 删除文件
+```
+DELETE /api/threads/{thread_id}/uploads/{filename}
+```
+
+**响应：**
+```json
+{
+  "success": true,
+  "message": "Deleted document.pdf"
+}
+```
+
+## 支持的文档格式
+
+以下格式会自动转换为 Markdown：
+- PDF (`.pdf`)
+- PowerPoint (`.ppt`, `.pptx`)
+- Excel (`.xls`, `.xlsx`)
+- Word (`.doc`, `.docx`)
+
+转换后的 Markdown 文件会保存在同一目录下，文件名为原文件名 + `.md` 扩展名。
+
+## Agent 集成
+
+### 自动文件列举
+
+Agent 在每次请求时会自动收到已上传文件的列表，格式如下：
+
+```xml
+<uploaded_files>
+The following files have been uploaded and are available for use:
+
+- document.pdf (1.2 MB)
+  Path: /mnt/user-data/uploads/document.pdf
+
+- document.md (45.3 KB)
+  Path: /mnt/user-data/uploads/document.md
+
+You can read these files using the `read_file` tool with the paths shown above.
+</uploaded_files>
+```
+
+### 使用上传的文件
+
+Agent 在沙箱中运行，使用虚拟路径访问文件。Agent 可以直接使用 `read_file` 工具读取上传的文件：
+
+```python
+# 读取原始 PDF（如果支持）
+read_file(path="/mnt/user-data/uploads/document.pdf")
+
+# 读取转换后的 Markdown（推荐）
+read_file(path="/mnt/user-data/uploads/document.md")
+```
+
+**路径映射关系：**
+- Agent 使用：`/mnt/user-data/uploads/document.pdf`（虚拟路径）
+- 实际存储：`backend/.deer-flow/threads/{thread_id}/user-data/uploads/document.pdf`
+- 前端访问：`/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/document.pdf`（HTTP URL）
+
+## 测试示例
+
+### 使用 curl 测试
+
+```bash
+# 1. 上传单个文件
+curl -X POST http://localhost:2026/api/threads/test-thread/uploads \
+  -F "files=@/path/to/document.pdf"
+
+# 2. 上传多个文件
+curl -X POST http://localhost:2026/api/threads/test-thread/uploads \
+  -F "files=@/path/to/document.pdf" \
+  -F "files=@/path/to/presentation.pptx" \
+  -F "files=@/path/to/spreadsheet.xlsx"
+
+# 3. 列出已上传文件
+curl http://localhost:2026/api/threads/test-thread/uploads/list
+
+# 4. 删除文件
+curl -X DELETE http://localhost:2026/api/threads/test-thread/uploads/document.pdf
+```
+
+### 使用 Python 测试
+
+```python
+import requests
+
+thread_id = "test-thread"
+base_url = "http://localhost:2026"
+
+# 上传文件
+files = [
+    ("files", open("document.pdf", "rb")),
+    ("files", open("presentation.pptx", "rb")),
+]
+response = requests.post(
+    f"{base_url}/api/threads/{thread_id}/uploads",
+    files=files
+)
+print(response.json())
+
+# 列出文件
+response = requests.get(f"{base_url}/api/threads/{thread_id}/uploads/list")
+print(response.json())
+
+# 删除文件
+response = requests.delete(
+    f"{base_url}/api/threads/{thread_id}/uploads/document.pdf"
+)
+print(response.json())
+```
+
+## 文件存储结构
+
+```
+backend/.deer-flow/threads/
+└── {thread_id}/
+    └── user-data/
+        └── uploads/
+            ├── document.pdf          # 原始文件
+            ├── document.md           # 转换后的 Markdown
+            ├── presentation.pptx
+            ├── presentation.md
+            └── ...
+```
+
+## 限制
+
+- 最大文件大小：100MB（可在 nginx.conf 中配置 `client_max_body_size`）
+- 文件名安全性：系统会自动验证文件路径，防止目录遍历攻击
+- 线程隔离：每个线程的上传文件相互隔离，无法跨线程访问
+
+## 技术实现
+
+### 组件
+
+1. **Upload Router** (`src/gateway/routers/uploads.py`)
+   - 处理文件上传、列表、删除请求
+   - 使用 markitdown 转换文档
+
+2. **Uploads Middleware** (`src/agents/middlewares/uploads_middleware.py`)
+   - 在每次 Agent 请求前注入文件列表
+   - 自动生成格式化的文件列表消息
+
+3. **Nginx 配置** (`nginx.conf`)
+   - 路由上传请求到 Gateway API
+   - 配置大文件上传支持
+
+### 依赖
+
+- `markitdown>=0.0.1a2` - 文档转换
+- `python-multipart>=0.0.20` - 文件上传处理
+
+## 故障排查
+
+### 文件上传失败
+
+1. 检查文件大小是否超过限制
+2. 检查 Gateway API 是否正常运行
+3. 检查磁盘空间是否充足
+4. 查看 Gateway 日志：`make gateway`
+
+### 文档转换失败
+
+1. 检查 markitdown 是否正确安装：`uv run python -c "import markitdown"`
+2. 查看日志中的具体错误信息
+3. 某些损坏或加密的文档可能无法转换，但原文件仍会保存
+
+### Agent 看不到上传的文件
+
+1. 确认 UploadsMiddleware 已在 agent.py 中注册
+2. 检查 thread_id 是否正确
+3. 确认文件确实已上传到正确的目录
+
+## 开发建议
+
+### 前端集成
+
+```typescript
+// 上传文件示例
+async function uploadFiles(threadId: string, files: File[]) {
+  const formData = new FormData();
+  files.forEach(file => {
+    formData.append('files', file);
+  });
+
+  const response = await fetch(
+    `/api/threads/${threadId}/uploads`,
+    {
+      method: 'POST',
+      body: formData,
+    }
+  );
+
+  return response.json();
+}
+
+// 列出文件
+async function listFiles(threadId: string) {
+  const response = await fetch(
+    `/api/threads/${threadId}/uploads/list`
+  );
+  return response.json();
+}
+```
+
+### 扩展功能建议
+
+1. **文件预览**：添加预览端点，支持在浏览器中直接查看文件
+2. **批量删除**：支持一次删除多个文件
+3. **文件搜索**：支持按文件名或类型搜索
+4. **版本控制**：保留文件的多个版本
+5. **压缩包支持**：自动解压 zip 文件
+6. **图片 OCR**：对上传的图片进行 OCR 识别

backend/docs/PATH_EXAMPLES.md

@@ -0,0 +1,289 @@
+# 文件路径使用示例
+
+## 三种路径类型
+
+DeerFlow 的文件上传系统返回三种不同的路径，每种路径用于不同的场景：
+
+### 1. 实际文件系统路径 (path)
+
+```
+.deer-flow/threads/{thread_id}/user-data/uploads/document.pdf
+```
+
+**用途：**
+- 文件在服务器文件系统中的实际位置
+- 相对于 `backend/` 目录
+- 用于直接文件系统访问、备份、调试等
+
+**示例：**
+```python
+# Python 代码中直接访问
+from pathlib import Path
+file_path = Path("backend/.deer-flow/threads/abc123/user-data/uploads/document.pdf")
+content = file_path.read_bytes()
+```
+
+### 2. 虚拟路径 (virtual_path)
+
+```
+/mnt/user-data/uploads/document.pdf
+```
+
+**用途：**
+- Agent 在沙箱环境中使用的路径
+- 沙箱系统会自动映射到实际路径
+- Agent 的所有文件操作工具都使用这个路径
+
+**示例：**
+Agent 在对话中使用：
+```python
+# Agent 使用 read_file 工具
+read_file(path="/mnt/user-data/uploads/document.pdf")
+
+# Agent 使用 bash 工具
+bash(command="cat /mnt/user-data/uploads/document.pdf")
+```
+
+### 3. HTTP 访问 URL (artifact_url)
+
+```
+/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/document.pdf
+```
+
+**用途：**
+- 前端通过 HTTP 访问文件
+- 用于下载、预览文件
+- 可以直接在浏览器中打开
+
+**示例：**
+```typescript
+// 前端 TypeScript/JavaScript 代码
+const threadId = 'abc123';
+const filename = 'document.pdf';
+
+// 下载文件
+const downloadUrl = `/api/threads/${threadId}/artifacts/mnt/user-data/uploads/${filename}?download=true`;
+window.open(downloadUrl);
+
+// 在新窗口预览
+const viewUrl = `/api/threads/${threadId}/artifacts/mnt/user-data/uploads/${filename}`;
+window.open(viewUrl, '_blank');
+
+// 使用 fetch API 获取
+const response = await fetch(viewUrl);
+const blob = await response.blob();
+```
+
+## 完整使用流程示例
+
+### 场景：前端上传文件并让 Agent 处理
+
+```typescript
+// 1. 前端上传文件
+async function uploadAndProcess(threadId: string, file: File) {
+  // 上传文件
+  const formData = new FormData();
+  formData.append('files', file);
+
+  const uploadResponse = await fetch(
+    `/api/threads/${threadId}/uploads`,
+    {
+      method: 'POST',
+      body: formData
+    }
+  );
+
+  const uploadData = await uploadResponse.json();
+  const fileInfo = uploadData.files[0];
+
+  console.log('文件信息：', fileInfo);
+  // {
+  //   filename: "report.pdf",
+  //   path: ".deer-flow/threads/abc123/user-data/uploads/report.pdf",
+  //   virtual_path: "/mnt/user-data/uploads/report.pdf",
+  //   artifact_url: "/api/threads/abc123/artifacts/mnt/user-data/uploads/report.pdf",
+  //   markdown_file: "report.md",
+  //   markdown_path: ".deer-flow/threads/abc123/user-data/uploads/report.md",
+  //   markdown_virtual_path: "/mnt/user-data/uploads/report.md",
+  //   markdown_artifact_url: "/api/threads/abc123/artifacts/mnt/user-data/uploads/report.md"
+  // }
+
+  // 2. 发送消息给 Agent
+  await sendMessage(threadId, "请分析刚上传的 PDF 文件");
+
+  // Agent 会自动看到文件列表，包含：
+  // - report.pdf (虚拟路径: /mnt/user-data/uploads/report.pdf)
+  // - report.md (虚拟路径: /mnt/user-data/uploads/report.md)
+
+  // 3. 前端可以直接访问转换后的 Markdown
+  const mdResponse = await fetch(fileInfo.markdown_artifact_url);
+  const markdownContent = await mdResponse.text();
+  console.log('Markdown 内容：', markdownContent);
+
+  // 4. 或者下载原始 PDF
+  const downloadLink = document.createElement('a');
+  downloadLink.href = fileInfo.artifact_url + '?download=true';
+  downloadLink.download = fileInfo.filename;
+  downloadLink.click();
+}
+```
+
+## 路径转换表
+
+| 场景 | 使用的路径类型 | 示例 |
+|------|---------------|------|
+| 服务器后端代码直接访问 | `path` | `.deer-flow/threads/abc123/user-data/uploads/file.pdf` |
+| Agent 工具调用 | `virtual_path` | `/mnt/user-data/uploads/file.pdf` |
+| 前端下载/预览 | `artifact_url` | `/api/threads/abc123/artifacts/mnt/user-data/uploads/file.pdf` |
+| 备份脚本 | `path` | `.deer-flow/threads/abc123/user-data/uploads/file.pdf` |
+| 日志记录 | `path` | `.deer-flow/threads/abc123/user-data/uploads/file.pdf` |
+
+## 代码示例集合
+
+### Python - 后端处理
+
+```python
+from pathlib import Path
+from src.agents.middlewares.thread_data_middleware import THREAD_DATA_BASE_DIR
+
+def process_uploaded_file(thread_id: str, filename: str):
+    # 使用实际路径
+    base_dir = Path.cwd() / THREAD_DATA_BASE_DIR / thread_id / "user-data" / "uploads"
+    file_path = base_dir / filename
+
+    # 直接读取
+    with open(file_path, 'rb') as f:
+        content = f.read()
+
+    return content
+```
+
+### JavaScript - 前端访问
+
+```javascript
+// 列出已上传的文件
+async function listUploadedFiles(threadId) {
+  const response = await fetch(`/api/threads/${threadId}/uploads/list`);
+  const data = await response.json();
+
+  // 为每个文件创建下载链接
+  data.files.forEach(file => {
+    console.log(`文件: ${file.filename}`);
+    console.log(`下载: ${file.artifact_url}?download=true`);
+    console.log(`预览: ${file.artifact_url}`);
+
+    // 如果是文档，还有 Markdown 版本
+    if (file.markdown_artifact_url) {
+      console.log(`Markdown: ${file.markdown_artifact_url}`);
+    }
+  });
+
+  return data.files;
+}
+
+// 删除文件
+async function deleteFile(threadId, filename) {
+  const response = await fetch(
+    `/api/threads/${threadId}/uploads/${filename}`,
+    { method: 'DELETE' }
+  );
+  return response.json();
+}
+```
+
+### React 组件示例
+
+```tsx
+import React, { useState, useEffect } from 'react';
+
+interface UploadedFile {
+  filename: string;
+  size: number;
+  path: string;
+  virtual_path: string;
+  artifact_url: string;
+  extension: string;
+  modified: number;
+  markdown_artifact_url?: string;
+}
+
+function FileUploadList({ threadId }: { threadId: string }) {
+  const [files, setFiles] = useState<UploadedFile[]>([]);
+
+  useEffect(() => {
+    fetchFiles();
+  }, [threadId]);
+
+  async function fetchFiles() {
+    const response = await fetch(`/api/threads/${threadId}/uploads/list`);
+    const data = await response.json();
+    setFiles(data.files);
+  }
+
+  async function handleUpload(event: React.ChangeEvent<HTMLInputElement>) {
+    const fileList = event.target.files;
+    if (!fileList) return;
+
+    const formData = new FormData();
+    Array.from(fileList).forEach(file => {
+      formData.append('files', file);
+    });
+
+    await fetch(`/api/threads/${threadId}/uploads`, {
+      method: 'POST',
+      body: formData
+    });
+
+    fetchFiles(); // 刷新列表
+  }
+
+  async function handleDelete(filename: string) {
+    await fetch(`/api/threads/${threadId}/uploads/${filename}`, {
+      method: 'DELETE'
+    });
+    fetchFiles(); // 刷新列表
+  }
+
+  return (
+    <div>
+      <input type="file" multiple onChange={handleUpload} />
+
+      <ul>
+        {files.map(file => (
+          <li key={file.filename}>
+            <span>{file.filename}</span>
+            <a href={file.artifact_url} target="_blank">预览</a>
+            <a href={`${file.artifact_url}?download=true`}>下载</a>
+            {file.markdown_artifact_url && (
+              <a href={file.markdown_artifact_url} target="_blank">Markdown</a>
+            )}
+            <button onClick={() => handleDelete(file.filename)}>删除</button>
+          </li>
+        ))}
+      </ul>
+    </div>
+  );
+}
+```
+
+## 注意事项
+
+1. **路径安全性**
+   - 实际路径（`path`）包含线程 ID，确保隔离
+   - API 会验证路径，防止目录遍历攻击
+   - 前端不应直接使用 `path`，而应使用 `artifact_url`
+
+2. **Agent 使用**
+   - Agent 只能看到和使用 `virtual_path`
+   - 沙箱系统自动映射到实际路径
+   - Agent 不需要知道实际的文件系统结构
+
+3. **前端集成**
+   - 始终使用 `artifact_url` 访问文件
+   - 不要尝试直接访问文件系统路径
+   - 使用 `?download=true` 参数强制下载
+
+4. **Markdown 转换**
+   - 转换成功时，会返回额外的 `markdown_*` 字段
+   - 建议优先使用 Markdown 版本（更易处理）
+   - 原始文件始终保留

backend/pyproject.toml

@@ -16,7 +16,9 @@ dependencies = [
     "langgraph>=1.0.6",
     "langgraph-cli[inmem]>=0.4.11",
     "markdownify>=1.2.2",
+    "markitdown[all,xlsx]>=0.0.1a2",
     "pydantic>=2.12.5",
+    "python-multipart>=0.0.20",
     "pyyaml>=6.0.3",
     "readabilipy>=0.3.0",
     "sse-starlette>=2.1.0",

backend/src/agents/lead_agent/agent.py

@@ -6,6 +6,7 @@ from src.agents.lead_agent.prompt import apply_prompt_template
 from src.agents.middlewares.clarification_middleware import ClarificationMiddleware
 from src.agents.middlewares.thread_data_middleware import ThreadDataMiddleware
 from src.agents.middlewares.title_middleware import TitleMiddleware
+from src.agents.middlewares.uploads_middleware import UploadsMiddleware
 from src.agents.thread_state import ThreadState
 from src.config.summarization_config import get_summarization_config
 from src.models import create_chat_model
@@ -170,6 +171,7 @@ Being proactive with task management demonstrates thoroughness and ensures all r
 
 
 # ThreadDataMiddleware must be before SandboxMiddleware to ensure thread_id is available
+# UploadsMiddleware should be after ThreadDataMiddleware to access thread_id
 # SummarizationMiddleware should be early to reduce context before other processing
 # TodoListMiddleware should be before ClarificationMiddleware to allow todo management
 # ClarificationMiddleware should be last to intercept clarification requests after model calls
@@ -182,7 +184,7 @@ def _build_middlewares(config: RunnableConfig):
     Returns:
         List of middleware instances.
     """
-    middlewares = [ThreadDataMiddleware(), SandboxMiddleware()]
+    middlewares = [ThreadDataMiddleware(), UploadsMiddleware(), SandboxMiddleware()]
 
     # Add summarization middleware if enabled
     summarization_middleware = _create_summarization_middleware()

backend/src/agents/lead_agent/prompt.py

@@ -104,12 +104,16 @@ You have access to skills that provide optimized workflows for specific tasks. E
 </skill_system>
 
 <working_directory existed="true">
-- User uploads: `/mnt/user-data/uploads`
-- User workspace: `/mnt/user-data/workspace`
-  - subagents: `/mnt/user-data/workspace/subagents`
-- Output files: `/mnt/user-data/outputs`
+- User uploads: `/mnt/user-data/uploads` - Files uploaded by the user (automatically listed in context)
+- User workspace: `/mnt/user-data/workspace` - Working directory for temporary files
+- Output files: `/mnt/user-data/outputs` - Final deliverables must be saved here
 
-All temporary work happens in `/mnt/user-data/workspace`. Final deliverables must be copied to `/mnt/user-data/outputs`.
+**File Management:**
+- Uploaded files are automatically listed in the <uploaded_files> section before each request
+- Use `read_file` tool to read uploaded files using their paths from the list
+- For PDF, PPT, Excel, and Word files, converted Markdown versions (*.md) are available alongside originals
+- All temporary work happens in `/mnt/user-data/workspace`
+- Final deliverables must be copied to `/mnt/user-data/outputs` and presented using `present_file` tool
 </working_directory>
 
 <response_style>

backend/src/agents/middlewares/uploads_middleware.py

@@ -0,0 +1,142 @@
+"""Middleware to inject uploaded files information into agent context."""
+
+import os
+from pathlib import Path
+from typing import NotRequired, override
+
+from langchain.agents import AgentState
+from langchain.agents.middleware import AgentMiddleware
+from langchain_core.messages import SystemMessage
+from langgraph.runtime import Runtime
+
+from src.agents.middlewares.thread_data_middleware import THREAD_DATA_BASE_DIR
+
+
+class UploadsMiddlewareState(AgentState):
+    """State schema for uploads middleware."""
+
+    uploaded_files: NotRequired[list[dict] | None]
+
+
+class UploadsMiddleware(AgentMiddleware[UploadsMiddlewareState]):
+    """Middleware to inject uploaded files information into the agent context.
+
+    This middleware lists all files in the thread's uploads directory and
+    adds a system message with the file list before the agent processes the request.
+    """
+
+    state_schema = UploadsMiddlewareState
+
+    def __init__(self, base_dir: str | None = None):
+        """Initialize the middleware.
+
+        Args:
+            base_dir: Base directory for thread data. Defaults to the current working directory.
+        """
+        super().__init__()
+        self._base_dir = base_dir or os.getcwd()
+
+    def _get_uploads_dir(self, thread_id: str) -> Path:
+        """Get the uploads directory for a thread.
+
+        Args:
+            thread_id: The thread ID.
+
+        Returns:
+            Path to the uploads directory.
+        """
+        return Path(self._base_dir) / THREAD_DATA_BASE_DIR / thread_id / "user-data" / "uploads"
+
+    def _list_uploaded_files(self, thread_id: str) -> list[dict]:
+        """List all files in the uploads directory.
+
+        Args:
+            thread_id: The thread ID.
+
+        Returns:
+            List of file information dictionaries.
+        """
+        uploads_dir = self._get_uploads_dir(thread_id)
+
+        if not uploads_dir.exists():
+            return []
+
+        files = []
+        for file_path in sorted(uploads_dir.iterdir()):
+            if file_path.is_file():
+                stat = file_path.stat()
+                files.append(
+                    {
+                        "filename": file_path.name,
+                        "size": stat.st_size,
+                        "path": f"/mnt/user-data/uploads/{file_path.name}",
+                        "extension": file_path.suffix,
+                    }
+                )
+
+        return files
+
+    def _create_files_message(self, files: list[dict]) -> str:
+        """Create a formatted message listing uploaded files.
+
+        Args:
+            files: List of file information dictionaries.
+
+        Returns:
+            Formatted string listing the files.
+        """
+        if not files:
+            return "<uploaded_files>\nNo files have been uploaded yet.\n</uploaded_files>"
+
+        lines = ["<uploaded_files>", "The following files have been uploaded and are available for use:", ""]
+
+        for file in files:
+            size_kb = file["size"] / 1024
+            if size_kb < 1024:
+                size_str = f"{size_kb:.1f} KB"
+            else:
+                size_str = f"{size_kb / 1024:.1f} MB"
+
+            lines.append(f"- {file['filename']} ({size_str})")
+            lines.append(f"  Path: {file['path']}")
+            lines.append("")
+
+        lines.append("You can read these files using the `read_file` tool with the paths shown above.")
+        lines.append("</uploaded_files>")
+
+        return "\n".join(lines)
+
+    @override
+    def before_agent(self, state: UploadsMiddlewareState, runtime: Runtime) -> dict | None:
+        """Inject uploaded files information before agent execution.
+
+        Args:
+            state: Current agent state.
+            runtime: Runtime context containing thread_id.
+
+        Returns:
+            State updates including uploaded files list.
+        """
+        thread_id = runtime.context.get("thread_id")
+        if thread_id is None:
+            return None
+
+        # List uploaded files
+        files = self._list_uploaded_files(thread_id)
+
+        # Create system message with file list
+        files_message = self._create_files_message(files)
+        system_message = SystemMessage(content=files_message)
+
+        # Inject the message into the message history
+        # This will be added after the system prompt but before user messages
+        messages = list(state.get("messages", []))
+
+        # Insert after the first system message (the main prompt)
+        insert_index = 1 if messages and hasattr(messages[0], "type") and messages[0].type == "system" else 0
+        messages.insert(insert_index, system_message)
+
+        return {
+            "uploaded_files": files,
+            "messages": messages,
+        }

backend/src/agents/thread_state.py

@@ -19,3 +19,4 @@ class ThreadState(AgentState):
     title: NotRequired[str | None]
     artifacts: NotRequired[list[str] | None]
     todos: NotRequired[list | None]
+    uploaded_files: NotRequired[list[dict] | None]

backend/src/gateway/app.py

@@ -5,7 +5,7 @@ from contextlib import asynccontextmanager
 from fastapi import FastAPI
 
 from src.gateway.config import get_gateway_config
-from src.gateway.routers import artifacts, mcp, models, skills
+from src.gateway.routers import artifacts, mcp, models, skills, uploads
 
 # Configure logging
 logging.basicConfig(
@@ -84,6 +84,10 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
                 "name": "artifacts",
                 "description": "Access and download thread artifacts and generated files",
             },
+            {
+                "name": "uploads",
+                "description": "Upload and manage user files for threads",
+            },
             {
                 "name": "health",
                 "description": "Health check and system status endpoints",
@@ -106,6 +110,9 @@ This gateway provides custom endpoints for models, MCP configuration, skills, an
     # Artifacts API is mounted at /api/threads/{thread_id}/artifacts
     app.include_router(artifacts.router)
 
+    # Uploads API is mounted at /api/threads/{thread_id}/uploads
+    app.include_router(uploads.router)
+
     @app.get("/health", tags=["health"])
     async def health_check() -> dict:
         """Health check endpoint.

backend/src/gateway/routers/__init__.py

@@ -1,3 +1,3 @@
-from . import artifacts, mcp, models
+from . import artifacts, mcp, models, skills, uploads
 
-__all__ = ["artifacts", "mcp", "models"]
+__all__ = ["artifacts", "mcp", "models", "skills", "uploads"]

backend/src/gateway/routers/uploads.py

@@ -0,0 +1,210 @@
+"""Upload router for handling file uploads."""
+
+import logging
+import os
+from pathlib import Path
+
+from fastapi import APIRouter, File, HTTPException, UploadFile
+from pydantic import BaseModel
+
+from src.agents.middlewares.thread_data_middleware import THREAD_DATA_BASE_DIR
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(prefix="/api/threads/{thread_id}/uploads", tags=["uploads"])
+
+# File extensions that should be converted to markdown
+CONVERTIBLE_EXTENSIONS = {
+    ".pdf",
+    ".ppt",
+    ".pptx",
+    ".xls",
+    ".xlsx",
+    ".doc",
+    ".docx",
+}
+
+
+class UploadResponse(BaseModel):
+    """Response model for file upload."""
+
+    success: bool
+    files: list[dict[str, str]]
+    message: str
+
+
+def get_uploads_dir(thread_id: str) -> Path:
+    """Get the uploads directory for a thread.
+
+    Args:
+        thread_id: The thread ID.
+
+    Returns:
+        Path to the uploads directory.
+    """
+    base_dir = Path(os.getcwd()) / THREAD_DATA_BASE_DIR / thread_id / "user-data" / "uploads"
+    base_dir.mkdir(parents=True, exist_ok=True)
+    return base_dir
+
+
+async def convert_file_to_markdown(file_path: Path) -> Path | None:
+    """Convert a file to markdown using markitdown.
+
+    Args:
+        file_path: Path to the file to convert.
+
+    Returns:
+        Path to the markdown file if conversion was successful, None otherwise.
+    """
+    try:
+        from markitdown import MarkItDown
+
+        md = MarkItDown()
+        result = md.convert(str(file_path))
+
+        # Save as .md file with same name
+        md_path = file_path.with_suffix(".md")
+        md_path.write_text(result.text_content, encoding="utf-8")
+
+        logger.info(f"Converted {file_path.name} to markdown: {md_path.name}")
+        return md_path
+    except Exception as e:
+        logger.error(f"Failed to convert {file_path.name} to markdown: {e}")
+        return None
+
+
+@router.post("", response_model=UploadResponse)
+async def upload_files(
+    thread_id: str,
+    files: list[UploadFile] = File(...),
+) -> UploadResponse:
+    """Upload multiple files to a thread's uploads directory.
+
+    For PDF, PPT, Excel, and Word files, they will be converted to markdown using markitdown.
+    All files (original and converted) are saved to /mnt/user-data/uploads.
+
+    Args:
+        thread_id: The thread ID to upload files to.
+        files: List of files to upload.
+
+    Returns:
+        Upload response with success status and file information.
+    """
+    if not files:
+        raise HTTPException(status_code=400, detail="No files provided")
+
+    uploads_dir = get_uploads_dir(thread_id)
+    uploaded_files = []
+
+    for file in files:
+        if not file.filename:
+            continue
+
+        try:
+            # Save the original file
+            file_path = uploads_dir / file.filename
+            content = await file.read()
+            file_path.write_bytes(content)
+
+            # Build relative path from backend root
+            relative_path = f".deer-flow/threads/{thread_id}/user-data/uploads/{file.filename}"
+
+            file_info = {
+                "filename": file.filename,
+                "size": str(len(content)),
+                "path": relative_path,  # Actual filesystem path (relative to backend/)
+                "virtual_path": f"/mnt/user-data/uploads/{file.filename}",  # Path for Agent in sandbox
+                "artifact_url": f"/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/{file.filename}",  # HTTP URL
+            }
+
+            logger.info(f"Saved file: {file.filename} ({len(content)} bytes) to {relative_path}")
+
+            # Check if file should be converted to markdown
+            file_ext = file_path.suffix.lower()
+            if file_ext in CONVERTIBLE_EXTENSIONS:
+                md_path = await convert_file_to_markdown(file_path)
+                if md_path:
+                    md_relative_path = f".deer-flow/threads/{thread_id}/user-data/uploads/{md_path.name}"
+                    file_info["markdown_file"] = md_path.name
+                    file_info["markdown_path"] = md_relative_path
+                    file_info["markdown_virtual_path"] = f"/mnt/user-data/uploads/{md_path.name}"
+                    file_info["markdown_artifact_url"] = f"/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/{md_path.name}"
+
+            uploaded_files.append(file_info)
+
+        except Exception as e:
+            logger.error(f"Failed to upload {file.filename}: {e}")
+            raise HTTPException(status_code=500, detail=f"Failed to upload {file.filename}: {str(e)}")
+
+    return UploadResponse(
+        success=True,
+        files=uploaded_files,
+        message=f"Successfully uploaded {len(uploaded_files)} file(s)",
+    )
+
+
+@router.get("/list", response_model=dict)
+async def list_uploaded_files(thread_id: str) -> dict:
+    """List all files in a thread's uploads directory.
+
+    Args:
+        thread_id: The thread ID to list files for.
+
+    Returns:
+        Dictionary containing list of files with their metadata.
+    """
+    uploads_dir = get_uploads_dir(thread_id)
+
+    if not uploads_dir.exists():
+        return {"files": [], "count": 0}
+
+    files = []
+    for file_path in sorted(uploads_dir.iterdir()):
+        if file_path.is_file():
+            stat = file_path.stat()
+            relative_path = f".deer-flow/threads/{thread_id}/user-data/uploads/{file_path.name}"
+            files.append(
+                {
+                    "filename": file_path.name,
+                    "size": stat.st_size,
+                    "path": relative_path,  # Actual filesystem path (relative to backend/)
+                    "virtual_path": f"/mnt/user-data/uploads/{file_path.name}",  # Path for Agent in sandbox
+                    "artifact_url": f"/api/threads/{thread_id}/artifacts/mnt/user-data/uploads/{file_path.name}",  # HTTP URL
+                    "extension": file_path.suffix,
+                    "modified": stat.st_mtime,
+                }
+            )
+
+    return {"files": files, "count": len(files)}
+
+
+@router.delete("/{filename}")
+async def delete_uploaded_file(thread_id: str, filename: str) -> dict:
+    """Delete a file from a thread's uploads directory.
+
+    Args:
+        thread_id: The thread ID.
+        filename: The filename to delete.
+
+    Returns:
+        Success message.
+    """
+    uploads_dir = get_uploads_dir(thread_id)
+    file_path = uploads_dir / filename
+
+    if not file_path.exists():
+        raise HTTPException(status_code=404, detail=f"File not found: {filename}")
+
+    # Security check: ensure the path is within the uploads directory
+    try:
+        file_path.resolve().relative_to(uploads_dir.resolve())
+    except ValueError:
+        raise HTTPException(status_code=403, detail="Access denied")
+
+    try:
+        file_path.unlink()
+        logger.info(f"Deleted file: {filename}")
+        return {"success": True, "message": f"Deleted {filename}"}
+    except Exception as e:
+        logger.error(f"Failed to delete {filename}: {e}")
+        raise HTTPException(status_code=500, detail=f"Failed to delete {filename}: {str(e)}")

backend/uv.lock

@@ -1,6 +1,14 @@
 version = 1
-revision = 3
+revision = 2
 requires-python = ">=3.12"
+resolution-markers = [
+    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version == '3.13.*' and sys_platform == 'win32'",
+    "python_full_version >= '3.14' and sys_platform != 'win32'",
+    "python_full_version == '3.13.*' and sys_platform != 'win32'",
+    "python_full_version < '3.13' and sys_platform == 'win32'",
+    "python_full_version < '3.13' and sys_platform != 'win32'",
+]
 
 [[package]]
 name = "agent-sandbox"
@@ -56,6 +64,105 @@ wheels = [
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 ]
 
+[[package]]
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+[[package]]
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 version = "9.0.2"
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 ]
 
+[[package]]
+name = "python-pptx"
+version = "1.0.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "lxml" },
+    { name = "pillow" },
+    { name = "typing-extensions" },
+    { name = "xlsxwriter" },
+]
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+
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 name = "pywin32"
 version = "311"
@@ -1858,6 +2460,20 @@ wheels = [
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 ]
 
+[[package]]
+name = "speechrecognition"
+version = "3.14.5"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "audioop-lts", marker = "python_full_version >= '3.13'" },
+    { name = "standard-aifc", marker = "python_full_version >= '3.13'" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/26/ab/bb1c60e7bfd6b7a736f76439b78ebbfb5e92a81b626b6e94a87e166f2ea4/speechrecognition-3.14.5.tar.gz", hash = "sha256:2d185192986b9b67a1502825a330e971f59a2cae0262f727a19ad1f6b586d00a", size = 32859817, upload-time = "2025-12-31T11:25:46.518Z" }
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 name = "sse-starlette"
 version = "2.1.3"
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 ]
 
+[[package]]
+name = "standard-aifc"
+version = "3.13.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "audioop-lts", marker = "python_full_version >= '3.13'" },
+    { name = "standard-chunk", marker = "python_full_version >= '3.13'" },
+]
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+]
+
+[[package]]
+name = "standard-chunk"
+version = "3.13.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/43/06/ce1bb165c1f111c7d23a1ad17204d67224baa69725bb6857a264db61beaf/standard_chunk-3.13.0.tar.gz", hash = "sha256:4ac345d37d7e686d2755e01836b8d98eda0d1a3ee90375e597ae43aaf064d654", size = 4672, upload-time = "2024-10-30T16:18:28.326Z" }
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+]
+
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 name = "starlette"
 version = "0.50.0"
@@ -1894,6 +2532,18 @@ wheels = [
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 ]
 
+[[package]]
+name = "sympy"
+version = "1.14.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "mpmath" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/83/d3/803453b36afefb7c2bb238361cd4ae6125a569b4db67cd9e79846ba2d68c/sympy-1.14.0.tar.gz", hash = "sha256:d3d3fe8df1e5a0b42f0e7bdf50541697dbe7d23746e894990c030e2b05e72517", size = 7793921, upload-time = "2025-04-27T18:05:01.611Z" }
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+]
+
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 name = "tavily-python"
 version = "0.7.17"
@@ -2006,6 +2656,15 @@ wheels = [
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 ]
 
+[[package]]
+name = "tzdata"
+version = "2025.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/5e/a7/c202b344c5ca7daf398f3b8a477eeb205cf3b6f32e7ec3a6bac0629ca975/tzdata-2025.3.tar.gz", hash = "sha256:de39c2ca5dc7b0344f2eba86f49d614019d29f060fc4ebc8a417896a620b56a7", size = 196772, upload-time = "2025-12-13T17:45:35.667Z" }
+wheels = [
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+]
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 version = "2.6.3"
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+[[package]]
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+version = "2.0.2"
+source = { registry = "https://pypi.org/simple" }
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+version = "3.2.9"
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+]
+
 [[package]]
 name = "xxhash"
 version = "3.6.0"
@@ -2315,6 +2992,19 @@ wheels = [
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+[[package]]
+name = "youtube-transcript-api"
+version = "1.0.3"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "defusedxml" },
+    { name = "requests" },
+]
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+]
+
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 name = "zipp"
 version = "3.23.0"

frontend/src/core/threads/hooks.ts

@@ -7,6 +7,7 @@ import { useCallback } from "react";
 import type { PromptInputMessage } from "@/components/ai-elements/prompt-input";
 
 import { getAPIClient } from "../api";
+import { uploadFiles } from "../uploads";
 
 import type {
   AgentThread,
@@ -72,6 +73,44 @@ export function useSubmitThread({
   const callback = useCallback(
     async (message: PromptInputMessage) => {
       const text = message.text.trim();
+
+      // Upload files first if any
+      if (message.files && message.files.length > 0) {
+        try {
+          // Convert FileUIPart to File objects by fetching blob URLs
+          const filePromises = message.files.map(async (fileUIPart) => {
+            if (fileUIPart.url && fileUIPart.filename) {
+              try {
+                // Fetch the blob URL to get the file data
+                const response = await fetch(fileUIPart.url);
+                const blob = await response.blob();
+
+                // Create a File object from the blob
+                return new File([blob], fileUIPart.filename, {
+                  type: fileUIPart.mediaType || blob.type,
+                });
+              } catch (error) {
+                console.error(`Failed to fetch file ${fileUIPart.filename}:`, error);
+                return null;
+              }
+            }
+            return null;
+          });
+
+          const files = (await Promise.all(filePromises)).filter(
+            (file): file is File => file !== null,
+          );
+
+          if (files.length > 0 && threadId) {
+            await uploadFiles(threadId, files);
+          }
+        } catch (error) {
+          console.error("Failed to upload files:", error);
+          // Continue with message submission even if upload fails
+          // You might want to show an error toast here
+        }
+      }
+
       await thread.submit(
         {
           messages: [

frontend/src/core/uploads/api.ts

@@ -0,0 +1,97 @@
+/**
+ * API functions for file uploads
+ */
+
+import { getBackendBaseURL } from "../config";
+
+export interface UploadedFileInfo {
+  filename: string;
+  size: number;
+  path: string;
+  virtual_path: string;
+  artifact_url: string;
+  extension?: string;
+  modified?: number;
+  markdown_file?: string;
+  markdown_path?: string;
+  markdown_virtual_path?: string;
+  markdown_artifact_url?: string;
+}
+
+export interface UploadResponse {
+  success: boolean;
+  files: UploadedFileInfo[];
+  message: string;
+}
+
+export interface ListFilesResponse {
+  files: UploadedFileInfo[];
+  count: number;
+}
+
+/**
+ * Upload files to a thread
+ */
+export async function uploadFiles(
+  threadId: string,
+  files: File[],
+): Promise<UploadResponse> {
+  const formData = new FormData();
+
+  files.forEach((file) => {
+    formData.append("files", file);
+  });
+
+  const response = await fetch(
+    `${getBackendBaseURL()}/api/threads/${threadId}/uploads`,
+    {
+      method: "POST",
+      body: formData,
+    },
+  );
+
+  if (!response.ok) {
+    const error = await response.json().catch(() => ({ detail: "Upload failed" }));
+    throw new Error(error.detail || "Upload failed");
+  }
+
+  return response.json();
+}
+
+/**
+ * List all uploaded files for a thread
+ */
+export async function listUploadedFiles(
+  threadId: string,
+): Promise<ListFilesResponse> {
+  const response = await fetch(
+    `${getBackendBaseURL()}/api/threads/${threadId}/uploads/list`,
+  );
+
+  if (!response.ok) {
+    throw new Error("Failed to list uploaded files");
+  }
+
+  return response.json();
+}
+
+/**
+ * Delete an uploaded file
+ */
+export async function deleteUploadedFile(
+  threadId: string,
+  filename: string,
+): Promise<{ success: boolean; message: string }> {
+  const response = await fetch(
+    `${getBackendBaseURL()}/api/threads/${threadId}/uploads/${filename}`,
+    {
+      method: "DELETE",
+    },
+  );
+
+  if (!response.ok) {
+    throw new Error("Failed to delete file");
+  }
+
+  return response.json();
+}

frontend/src/core/uploads/hooks.ts

@@ -0,0 +1,79 @@
+/**
+ * React hooks for file uploads
+ */
+
+import { useMutation, useQuery, useQueryClient } from "@tanstack/react-query";
+import { useCallback } from "react";
+
+import {
+  deleteUploadedFile,
+  listUploadedFiles,
+  uploadFiles,
+  type UploadedFileInfo,
+  type UploadResponse,
+} from "./api";
+
+/**
+ * Hook to upload files
+ */
+export function useUploadFiles(threadId: string) {
+  const queryClient = useQueryClient();
+
+  return useMutation<UploadResponse, Error, File[]>({
+    mutationFn: (files: File[]) => uploadFiles(threadId, files),
+    onSuccess: () => {
+      // Invalidate the uploaded files list
+      void queryClient.invalidateQueries({
+        queryKey: ["uploads", "list", threadId],
+      });
+    },
+  });
+}
+
+/**
+ * Hook to list uploaded files
+ */
+export function useUploadedFiles(threadId: string) {
+  return useQuery({
+    queryKey: ["uploads", "list", threadId],
+    queryFn: () => listUploadedFiles(threadId),
+    enabled: !!threadId,
+  });
+}
+
+/**
+ * Hook to delete an uploaded file
+ */
+export function useDeleteUploadedFile(threadId: string) {
+  const queryClient = useQueryClient();
+
+  return useMutation({
+    mutationFn: (filename: string) => deleteUploadedFile(threadId, filename),
+    onSuccess: () => {
+      // Invalidate the uploaded files list
+      void queryClient.invalidateQueries({
+        queryKey: ["uploads", "list", threadId],
+      });
+    },
+  });
+}
+
+/**
+ * Hook to handle file uploads in submit flow
+ * Returns a function that uploads files and returns their info
+ */
+export function useUploadFilesOnSubmit(threadId: string) {
+  const uploadMutation = useUploadFiles(threadId);
+
+  return useCallback(
+    async (files: File[]): Promise<UploadedFileInfo[]> => {
+      if (files.length === 0) {
+        return [];
+      }
+
+      const result = await uploadMutation.mutateAsync(files);
+      return result.files;
+    },
+    [uploadMutation],
+  );
+}

frontend/src/core/uploads/index.ts

@@ -0,0 +1,6 @@
+/**
+ * File uploads module
+ */
+
+export * from "./api";
+export * from "./hooks";

nginx.conf

@@ -115,6 +115,20 @@ http {
             proxy_set_header X-Forwarded-Proto $scheme;
         }
 
+        # Custom API: Uploads endpoint
+        location ~ ^/api/threads/[^/]+/uploads {
+            proxy_pass http://gateway;
+            proxy_http_version 1.1;
+            proxy_set_header Host $host;
+            proxy_set_header X-Real-IP $remote_addr;
+            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+            proxy_set_header X-Forwarded-Proto $scheme;
+
+            # Large file upload support
+            client_max_body_size 100M;
+            proxy_request_buffering off;
+        }
+
         # API Documentation: Swagger UI
         location /docs {
             proxy_pass http://gateway;