diff --git a/fastapi_app.py b/fastapi_app.py
index 5bc2d2d..b1fdf28 100644
--- a/fastapi_app.py
+++ b/fastapi_app.py
@@ -1,5 +1,8 @@
 import json
 import os
+import aiofiles
+import aiohttp
+import hashlib
 from typing import AsyncGenerator, Dict, List, Optional, Union
 
 import uvicorn
@@ -41,19 +44,345 @@ def get_content_from_messages(messages: List[dict]) -> str:
 
 from file_loaded_agent_manager import get_global_agent_manager, init_global_agent_manager
 from gbase_agent import update_agent_llm
-from zip_project_handler import zip_handler
 
 
-def get_zip_url_from_unique_id(unique_id: str) -> Optional[str]:
-    """从unique_map.json中读取zip_url"""
+async def download_file(url: str, destination_path: str) -> bool:
+    """Download file from URL to destination path"""
     try:
-        with open('unique_map.json', 'r', encoding='utf-8') as f:
-            unique_map = json.load(f)
-        return unique_map.get(unique_id)
+        os.makedirs(os.path.dirname(destination_path), exist_ok=True)
+        async with aiohttp.ClientSession() as session:
+            async with session.get(url) as response:
+                if response.status == 200:
+                    async with aiofiles.open(destination_path, 'wb') as f:
+                        async for chunk in response.content.iter_chunked(8192):
+                            await f.write(chunk)
+                    return True
+                else:
+                    print(f"Failed to download file from {url}, status: {response.status}")
+                    return False
     except Exception as e:
-        print(f"Error reading unique_map.json: {e}")
+        print(f"Error downloading file from {url}: {str(e)}")
+        return False
+
+
+def get_file_hash(file_path: str) -> str:
+    """Generate MD5 hash for a file path/URL"""
+    return hashlib.md5(file_path.encode('utf-8')).hexdigest()
+
+def load_processed_files_log(unique_id: str) -> Dict[str, Dict]:
+    """Load processed files log for a project"""
+    log_file = os.path.join("projects", unique_id, "processed_files.json")
+    if os.path.exists(log_file):
+        try:
+            with open(log_file, 'r', encoding='utf-8') as f:
+                return json.load(f)
+        except Exception as e:
+            print(f"Error loading processed files log: {str(e)}")
+    return {}
+
+def save_processed_files_log(unique_id: str, processed_log: Dict[str, Dict]):
+    """Save processed files log for a project"""
+    log_file = os.path.join("projects", unique_id, "processed_files.json")
+    try:
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
+        with open(log_file, 'w', encoding='utf-8') as f:
+            json.dump(processed_log, f, ensure_ascii=False, indent=2)
+    except Exception as e:
+        print(f"Error saving processed files log: {str(e)}")
+
+def remove_file_or_directory(path: str):
+    """Remove file or directory if it exists"""
+    if os.path.exists(path):
+        try:
+            if os.path.isdir(path):
+                import shutil
+                shutil.rmtree(path)
+                print(f"Removed directory: {path}")
+            else:
+                os.remove(path)
+                print(f"Removed file: {path}")
+            return True
+        except Exception as e:
+            print(f"Error removing {path}: {str(e)}")
+    return False
+
+def remove_dataset_directory(unique_id: str, filename_without_ext: str):
+    """Remove the entire dataset directory for a specific file"""
+    dataset_dir = os.path.join("projects", unique_id, "dataset", filename_without_ext)
+    if remove_file_or_directory(dataset_dir):
+        print(f"Removed dataset directory: {dataset_dir}")
+        return True
+    return False
+
+def get_document_preview(document_path: str, max_lines: int = 10) -> str:
+    """Get preview of document content (first max_lines lines)"""
+    try:
+        with open(document_path, 'r', encoding='utf-8') as f:
+            lines = []
+            for i, line in enumerate(f):
+                if i >= max_lines:
+                    break
+                lines.append(line.rstrip())
+            return '\n'.join(lines)
+    except Exception as e:
+        print(f"Error reading document preview from {document_path}: {str(e)}")
+        return f"Error reading document: {str(e)}"
+
+def generate_dataset_structure(unique_id: str) -> str:
+    """Generate dataset directory structure as a string"""
+    dataset_dir = os.path.join("projects", unique_id, "dataset")
+    structure_lines = []
+    
+    def build_tree(path: str, prefix: str = "", is_last: bool = True):
+        try:
+            items = sorted(os.listdir(path))
+            items = [item for item in items if not item.startswith('.')]  # Hide hidden files
+            
+            for i, item in enumerate(items):
+                item_path = os.path.join(path, item)
+                is_dir = os.path.isdir(item_path)
+                
+                # Determine tree symbols
+                if i == len(items) - 1:
+                    current_prefix = "└── " if is_last else "├── "
+                    next_prefix = "    " if is_last else "│   "
+                else:
+                    current_prefix = "├── "
+                    next_prefix = "│   "
+                
+                line = prefix + current_prefix + item
+                if is_dir:
+                    line += "/"
+                structure_lines.append(line)
+                
+                # Recursively process subdirectories
+                if is_dir:
+                    build_tree(item_path, prefix + next_prefix, i == len(items) - 1)
+                    
+        except Exception as e:
+            print(f"Error building tree for {path}: {str(e)}")
+    
+    structure_lines.append("dataset/")
+    if os.path.exists(dataset_dir):
+        build_tree(dataset_dir)
+    else:
+        structure_lines.append("    (empty)")
+    
+    return '\n'.join(structure_lines)
+
+def generate_project_readme(unique_id: str) -> str:
+    """Generate README.md content for a project"""
+    project_dir = os.path.join("projects", unique_id)
+    dataset_dir = os.path.join(project_dir, "dataset")
+    
+    readme_content = f"""# Project: {unique_id}
+
+## Dataset Structure
+
+```
+{generate_dataset_structure(unique_id)}
+```
+
+## Files Description
+
+"""
+    
+    if not os.path.exists(dataset_dir):
+        readme_content += "No dataset files available.\n"
+    else:
+        # Get all document directories
+        doc_dirs = []
+        try:
+            for item in sorted(os.listdir(dataset_dir)):
+                item_path = os.path.join(dataset_dir, item)
+                if os.path.isdir(item_path):
+                    doc_dirs.append(item)
+        except Exception as e:
+            print(f"Error listing dataset directories: {str(e)}")
+        
+        if not doc_dirs:
+            readme_content += "No document directories found.\n"
+        else:
+            for doc_dir in doc_dirs:
+                doc_path = os.path.join(dataset_dir, doc_dir)
+                document_file = os.path.join(doc_path, "document.txt")
+                pagination_file = os.path.join(doc_path, "pagination.txt")
+                embeddings_file = os.path.join(doc_path, "document_embeddings.pkl")
+                
+                readme_content += f"### {doc_dir}\n\n"
+                readme_content += f"**Files:**\n"
+                readme_content += f"- `document.txt`"
+                if os.path.exists(document_file):
+                    readme_content += " ✓"
+                readme_content += "\n"
+                
+                readme_content += f"- `pagination.txt`"
+                if os.path.exists(pagination_file):
+                    readme_content += " ✓"
+                readme_content += "\n"
+                
+                readme_content += f"- `document_embeddings.pkl`"
+                if os.path.exists(embeddings_file):
+                    readme_content += " ✓"
+                readme_content += "\n\n"
+                
+                # Add document preview
+                if os.path.exists(document_file):
+                    readme_content += f"**Content Preview (first 10 lines):**\n\n```\n"
+                    preview = get_document_preview(document_file, 10)
+                    readme_content += preview
+                    readme_content += "\n```\n\n"
+                else:
+                    readme_content += f"**Content Preview:** Not available\n\n"
+    
+    readme_content += f"""---
+*Generated on {__import__('datetime').datetime.now().strftime('%Y-%m-%d %H:%M:%S')}*
+"""
+    
+    return readme_content
+
+def save_project_readme(unique_id: str):
+    """Generate and save README.md for a project"""
+    try:
+        readme_content = generate_project_readme(unique_id)
+        readme_path = os.path.join("projects", unique_id, "README.md")
+        
+        with open(readme_path, 'w', encoding='utf-8') as f:
+            f.write(readme_content)
+        
+        print(f"Generated README.md for project {unique_id}")
+        return readme_path
+    except Exception as e:
+        print(f"Error generating README for project {unique_id}: {str(e)}")
         return None
 
+async def download_dataset_files(unique_id: str, files: List[str]) -> List[str]:
+    """Download or copy dataset files to projects/{unique_id}/files directory with processing state management"""
+    if not files:
+        return []
+    
+    # Load existing processed files log
+    processed_log = load_processed_files_log(unique_id)
+    files_dir = os.path.join("projects", unique_id, "files")
+    
+    # Convert files list to a set for easy comparison
+    new_files_hashes = {get_file_hash(file_path): file_path for file_path in files}
+    existing_files_hashes = set(processed_log.keys())
+    
+    # Files to process (new or modified)
+    files_to_process = []
+    # Files to remove (no longer in the list)
+    files_to_remove = existing_files_hashes - set(new_files_hashes.keys())
+    
+    processed_files = []
+    
+    # Remove files that are no longer in the list
+    for file_hash in files_to_remove:
+        file_info = processed_log[file_hash]
+        
+        # Remove local file in files directory
+        if 'local_path' in file_info:
+            remove_file_or_directory(file_info['local_path'])
+        
+        # Remove the entire dataset directory for this file
+        if 'filename' in file_info:
+            filename_without_ext = os.path.splitext(file_info['filename'])[0]
+            remove_dataset_directory(unique_id, filename_without_ext)
+        
+        # Also remove any specific dataset path if exists (fallback)
+        if 'dataset_path' in file_info:
+            remove_file_or_directory(file_info['dataset_path'])
+        
+        # Remove from log
+        del processed_log[file_hash]
+        print(f"Removed file from processing: {file_info.get('original_path', 'unknown')}")
+    
+    # Process new files
+    for file_path in files:
+        file_hash = get_file_hash(file_path)
+        
+        # Check if file was already processed
+        if file_hash in processed_log:
+            file_info = processed_log[file_hash]
+            if 'local_path' in file_info and os.path.exists(file_info['local_path']):
+                processed_files.append(file_info['local_path'])
+                print(f"Skipped already processed file: {file_path}")
+                continue
+        
+        # Extract filename from URL or path
+        filename = file_path.split("/")[-1]
+        if not filename:
+            filename = f"file_{len(processed_files)}"
+        
+        destination_path = os.path.join(files_dir, filename)
+        
+        # Check if it's a URL (remote file) or local file
+        success = False
+        if file_path.startswith(('http://', 'https://')):
+            # Download remote file
+            success = await download_file(file_path, destination_path)
+        else:
+            # Copy local file
+            try:
+                import shutil
+                os.makedirs(files_dir, exist_ok=True)
+                shutil.copy2(file_path, destination_path)
+                success = True
+                print(f"Copied local file: {file_path} -> {destination_path}")
+            except Exception as e:
+                print(f"Failed to copy local file {file_path}: {str(e)}")
+        
+        if success:
+            processed_files.append(destination_path)
+            # Update processed log
+            processed_log[file_hash] = {
+                'original_path': file_path,
+                'local_path': destination_path,
+                'filename': filename,
+                'processed_at': str(__import__('datetime').datetime.now()),
+                'file_type': 'remote' if file_path.startswith(('http://', 'https://')) else 'local'
+            }
+            print(f"Successfully processed file: {file_path}")
+        else:
+            print(f"Failed to process file: {file_path}")
+    
+    # After downloading/copying files, organize them into dataset structure
+    if processed_files:
+        try:
+            from organize_dataset_files import organize_single_project_files
+            
+            # Update dataset paths in the log after organization
+            old_processed_log = processed_log.copy()
+            organize_single_project_files(unique_id, skip_processed=True)
+            
+            # Try to update dataset paths in the log
+            for file_hash, file_info in old_processed_log.items():
+                if 'local_path' in file_info and os.path.exists(file_info['local_path']):
+                    # Construct expected dataset path based on known structure
+                    filename_without_ext = os.path.splitext(file_info['filename'])[0]
+                    dataset_path = os.path.join("projects", unique_id, "dataset", filename_without_ext, "document.txt")
+                    if os.path.exists(dataset_path):
+                        processed_log[file_hash]['dataset_path'] = dataset_path
+            
+            print(f"Organized files for project {unique_id} into dataset structure (skipping already processed files)")
+        except Exception as e:
+            print(f"Failed to organize files for project {unique_id}: {str(e)}")
+    
+    # Save the updated processed log
+    save_processed_files_log(unique_id, processed_log)
+    
+    # Generate README.md after processing files
+    try:
+        save_project_readme(unique_id)
+    except Exception as e:
+        print(f"Failed to generate README for project {unique_id}: {str(e)}")
+    
+    return processed_files
+
+
+
+
+
 # 全局助手管理器配置
 max_cached_agents = int(os.getenv("MAX_CACHED_AGENTS", "20"))
 
@@ -80,11 +409,17 @@ class Message(BaseModel):
     content: str
 
 
+class DatasetRequest(BaseModel):
+    system_prompt: Optional[str] = None
+    mcp_settings: Optional[List[Dict]] = None
+    files: Optional[List[str]] = None
+    unique_id: Optional[str] = None
+
+
 class ChatRequest(BaseModel):
     messages: List[Message]
     model: str = "qwen3-next"
     model_server: str = ""
-    zip_url: Optional[str] = None
     unique_id: Optional[str] = None
     stream: Optional[bool] = False
     
@@ -170,13 +505,102 @@ async def generate_stream_response(agent, messages, request) -> AsyncGenerator[s
         yield f"data: {json.dumps(error_data, ensure_ascii=False)}\n\n"
 
 
+class FileProcessRequest(BaseModel):
+    unique_id: str
+    files: Optional[List[str]] = None
+    system_prompt: Optional[str] = None
+    mcp_settings: Optional[List[Dict]] = None
+    
+    class Config:
+        extra = 'allow'
+
+
+class FileProcessResponse(BaseModel):
+    success: bool
+    message: str
+    unique_id: str
+    processed_files: List[str]
+
+
+@app.post("/api/v1/files/process")
+async def process_files(request: FileProcessRequest, authorization: Optional[str] = Header(None)):
+    """
+    Process dataset files for a given unique_id
+    
+    Args:
+        request: FileProcessRequest containing unique_id, files, system_prompt, and mcp_settings
+        authorization: Authorization header containing API key (Bearer <API_KEY>)
+        
+    Returns:
+        FileProcessResponse: Processing result with file list
+    """
+    try:
+
+        unique_id = request.unique_id
+        if not unique_id:
+            raise HTTPException(status_code=400, detail="unique_id is required")
+        
+        # 处理文件：只使用request.files
+        processed_files = []
+        if request.files:
+            # 使用请求中的文件
+            processed_files = await download_dataset_files(unique_id, request.files)
+            print(f"Processed {len(processed_files)} dataset files for unique_id: {unique_id}")
+        else:
+            print(f"No files provided in request for unique_id: {unique_id}")
+        
+        # 使用unique_id获取项目目录
+        project_dir = os.path.join("projects", unique_id)
+        if not os.path.exists(project_dir):
+            raise HTTPException(status_code=400, detail=f"Project directory not found for unique_id: {unique_id}")
+        
+        # 收集项目目录下所有的 document.txt 文件
+        document_files = []
+        for root, dirs, files in os.walk(project_dir):
+            for file in files:
+                if file == "document.txt":
+                    document_files.append(os.path.join(root, file))
+        
+        # 合并所有处理的文件
+        all_files = document_files + processed_files
+        
+        if not all_files:
+            print(f"警告: 项目目录 {project_dir} 中未找到任何 document.txt 文件")
+        
+        # 保存system_prompt和mcp_settings到项目目录（如果提供）
+        if request.system_prompt:
+            system_prompt_file = os.path.join(project_dir, "system_prompt.md")
+            with open(system_prompt_file, 'w', encoding='utf-8') as f:
+                f.write(request.system_prompt)
+            print(f"Saved system_prompt for unique_id: {unique_id}")
+        
+        if request.mcp_settings:
+            mcp_settings_file = os.path.join(project_dir, "mcp_settings.json")
+            with open(mcp_settings_file, 'w', encoding='utf-8') as f:
+                json.dump(request.mcp_settings, f, ensure_ascii=False, indent=2)
+            print(f"Saved mcp_settings for unique_id: {unique_id}")
+        
+        return FileProcessResponse(
+            success=True,
+            message=f"Successfully processed {len(all_files)} files",
+            unique_id=unique_id,
+            processed_files=all_files
+        )
+        
+    except HTTPException:
+        raise
+    except Exception as e:
+        print(f"Error processing files: {str(e)}")
+        raise HTTPException(status_code=500, detail=f"Internal server error: {str(e)}")
+
+
 @app.post("/api/v1/chat/completions")
 async def chat_completions(request: ChatRequest, authorization: Optional[str] = Header(None)):
     """
     Chat completions API similar to OpenAI, supports both streaming and non-streaming
     
     Args:
-        request: ChatRequest containing messages, model, zip_url, etc.
+        request: ChatRequest containing messages, model, dataset with unique_id, system_prompt, mcp_settings, and files
         authorization: Authorization header containing API key (Bearer <API_KEY>)
         
     Returns:
@@ -192,39 +616,23 @@ async def chat_completions(request: ChatRequest, authorization: Optional[str] =
             else:
                 api_key = authorization
         
-        # 从最外层获取zip_url和unique_id参数
-        zip_url = request.zip_url
+        # 获取unique_id
         unique_id = request.unique_id
+        if not unique_id:
+            raise HTTPException(status_code=400, detail="unique_id is required")
         
-        # 如果提供了unique_id，从unique_map.json中读取zip_url
-        if unique_id:
-            zip_url = get_zip_url_from_unique_id(unique_id)
-            if not zip_url:
-                raise HTTPException(status_code=400, detail=f"No zip_url found for unique_id: {unique_id}")
-        
-        if not zip_url:
-            raise HTTPException(status_code=400, detail="zip_url is required")
-        
-        # 使用ZIP URL获取项目数据
-        print(f"从ZIP URL加载项目: {zip_url}")
-        project_dir = zip_handler.get_project_from_zip(zip_url, unique_id if unique_id else None)
-        if not project_dir:
-            raise HTTPException(status_code=400, detail=f"Failed to load project from ZIP URL: {zip_url}")
-        
-        # 收集项目目录下所有的 document.txt 文件
-        document_files = zip_handler.collect_document_files(project_dir)
-        
-        if not document_files:
-            print(f"警告: 项目目录 {project_dir} 中未找到任何 document.txt 文件")
+        # 使用unique_id获取项目目录
+        project_dir = os.path.join("projects", unique_id)
+        if not os.path.exists(project_dir):
+            raise HTTPException(status_code=400, detail=f"Project directory not found for unique_id: {unique_id}")
         
         # 收集额外参数作为 generate_cfg
-        exclude_fields = {'messages', 'model', 'model_server', 'zip_url', 'unique_id', 'stream'}
+        exclude_fields = {'messages', 'model', 'model_server', 'unique_id', 'stream'}
         generate_cfg = {k: v for k, v in request.model_dump().items() if k not in exclude_fields}
         
-        # 从全局管理器获取或创建文件预加载的助手实例
+        # 从全局管理器获取或创建助手实例（配置读取逻辑已在agent_manager内部处理）
         agent = await agent_manager.get_or_create_agent(
-            zip_url=zip_url,
-            files=document_files,
+            unique_id=unique_id,
             project_dir=project_dir,
             model_name=request.model,
             api_key=api_key,
@@ -322,17 +730,13 @@ async def system_status():
 
 @app.post("/system/cleanup-cache")
 async def cleanup_cache():
-    """清理ZIP文件缓存和助手缓存"""
+    """清理助手缓存"""
     try:
-        # 清理ZIP文件缓存
-        zip_handler.cleanup_cache()
-        
         # 清理助手实例缓存
         cleared_count = agent_manager.clear_cache()
         
         return {
             "message": "缓存清理成功",
-            "cleared_zip_files": True,
             "cleared_agent_instances": cleared_count
         }
     except Exception as e:
@@ -356,11 +760,9 @@ async def cleanup_agent_cache():
 async def get_cached_projects():
     """获取所有缓存的项目信息"""
     try:
-        cached_urls = agent_manager.list_cached_zip_urls()
         cache_stats = agent_manager.get_cache_stats()
         
         return {
-            "cached_projects": cached_urls,
             "cache_stats": cache_stats
         }
     except Exception as e:
@@ -368,18 +770,108 @@ async def get_cached_projects():
 
 
 @app.post("/system/remove-project-cache")
-async def remove_project_cache(zip_url: str):
+async def remove_project_cache(unique_id: str):
     """移除特定项目的缓存"""
     try:
-        success = agent_manager.remove_cache_by_url(zip_url)
+        success = agent_manager.remove_cache_by_unique_id(unique_id)
         if success:
-            return {"message": f"项目缓存移除成功: {zip_url}"}
+            return {"message": f"项目缓存移除成功: {unique_id}"}
         else:
-            return {"message": f"未找到项目缓存: {zip_url}", "removed": False}
+            return {"message": f"未找到项目缓存: {unique_id}", "removed": False}
     except Exception as e:
         raise HTTPException(status_code=500, detail=f"移除项目缓存失败: {str(e)}")
 
 
+@app.get("/api/v1/files/{unique_id}/status")
+async def get_files_processing_status(unique_id: str):
+    """获取项目的文件处理状态"""
+    try:
+        # Load processed files log
+        processed_log = load_processed_files_log(unique_id)
+        
+        # Get project directory info
+        project_dir = os.path.join("projects", unique_id)
+        project_exists = os.path.exists(project_dir)
+        
+        # Collect document.txt files
+        document_files = []
+        if project_exists:
+            for root, dirs, files in os.walk(project_dir):
+                for file in files:
+                    if file == "document.txt":
+                        document_files.append(os.path.join(root, file))
+        
+        return {
+            "unique_id": unique_id,
+            "project_exists": project_exists,
+            "processed_files_count": len(processed_log),
+            "processed_files": processed_log,
+            "document_files_count": len(document_files),
+            "document_files": document_files,
+            "log_file_exists": os.path.exists(os.path.join("projects", unique_id, "processed_files.json"))
+        }
+    except Exception as e:
+        raise HTTPException(status_code=500, detail=f"获取文件处理状态失败: {str(e)}")
+
+
+@app.post("/api/v1/files/{unique_id}/reset")
+async def reset_files_processing(unique_id: str):
+    """重置项目的文件处理状态，删除处理日志和所有文件"""
+    try:
+        project_dir = os.path.join("projects", unique_id)
+        log_file = os.path.join("projects", unique_id, "processed_files.json")
+        
+        # Load processed log to know what files to remove
+        processed_log = load_processed_files_log(unique_id)
+        
+        removed_files = []
+        # Remove all processed files and their dataset directories
+        for file_hash, file_info in processed_log.items():
+            # Remove local file in files directory
+            if 'local_path' in file_info:
+                if remove_file_or_directory(file_info['local_path']):
+                    removed_files.append(file_info['local_path'])
+            
+            # Remove the entire dataset directory for this file
+            if 'filename' in file_info:
+                filename_without_ext = os.path.splitext(file_info['filename'])[0]
+                dataset_dir = os.path.join("projects", unique_id, "dataset", filename_without_ext)
+                if remove_file_or_directory(dataset_dir):
+                    removed_files.append(dataset_dir)
+            
+            # Also remove any specific dataset path if exists (fallback)
+            if 'dataset_path' in file_info:
+                if remove_file_or_directory(file_info['dataset_path']):
+                    removed_files.append(file_info['dataset_path'])
+        
+        # Remove the log file
+        if remove_file_or_directory(log_file):
+            removed_files.append(log_file)
+        
+        # Remove the entire files directory
+        files_dir = os.path.join(project_dir, "files")
+        if remove_file_or_directory(files_dir):
+            removed_files.append(files_dir)
+        
+        # Also remove the entire dataset directory (clean up any remaining files)
+        dataset_dir = os.path.join(project_dir, "dataset")
+        if remove_file_or_directory(dataset_dir):
+            removed_files.append(dataset_dir)
+        
+        # Remove README.md if exists
+        readme_file = os.path.join(project_dir, "README.md")
+        if remove_file_or_directory(readme_file):
+            removed_files.append(readme_file)
+        
+        return {
+            "message": f"文件处理状态重置成功: {unique_id}",
+            "removed_files_count": len(removed_files),
+            "removed_files": removed_files
+        }
+    except Exception as e:
+        raise HTTPException(status_code=500, detail=f"重置文件处理状态失败: {str(e)}")
+
+
 
 
 if __name__ == "__main__":
diff --git a/file_loaded_agent_manager.py b/file_loaded_agent_manager.py
index 1e69656..e4d838c 100644
--- a/file_loaded_agent_manager.py
+++ b/file_loaded_agent_manager.py
@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""文件预加载助手管理器 - 管理基于ZIP URL的助手实例缓存"""
+"""文件预加载助手管理器 - 管理基于unique_id的助手实例缓存"""
 
 import hashlib
 import time
@@ -27,20 +27,19 @@ from gbase_agent import init_agent_service_with_files, update_agent_llm
 class FileLoadedAgentManager:
     """文件预加载助手管理器
     
-    基于 ZIP URL 缓存助手实例，避免重复创建和文件解析
+    基于 unique_id 缓存助手实例，避免重复创建和文件解析
     """
     
     def __init__(self, max_cached_agents: int = 20):
-        self.agents: Dict[str, Assistant] = {}  # {zip_url_hash: assistant_instance}
-        self.zip_urls: Dict[str, str] = {}  # {zip_url_hash: original_zip_url}
+        self.agents: Dict[str, Assistant] = {}  # {unique_id: assistant_instance}
+        self.unique_ids: Dict[str, str] = {}  # {cache_key: unique_id}
         self.access_times: Dict[str, float] = {}  # LRU 访问时间管理
         self.creation_times: Dict[str, float] = {}  # 创建时间记录
-        self.file_counts: Dict[str, int] = {}  # 缓存的文件数量
         self.max_cached_agents = max_cached_agents
     
-    def _get_zip_url_hash(self, zip_url: str) -> str:
-        """获取 ZIP URL 的哈希值作为缓存键"""
-        return hashlib.md5(zip_url.encode('utf-8')).hexdigest()[:16]
+    def _get_cache_key(self, unique_id: str) -> str:
+        """获取 unique_id 的哈希值作为缓存键"""
+        return hashlib.md5(unique_id.encode('utf-8')).hexdigest()[:16]
     
     def _update_access_time(self, cache_key: str):
         """更新访问时间（LRU 管理）"""
@@ -60,10 +59,9 @@ class FileLoadedAgentManager:
         for cache_key in keys_to_remove:
             try:
                 del self.agents[cache_key]
-                del self.zip_urls[cache_key]
+                del self.unique_ids[cache_key]
                 del self.access_times[cache_key]
                 del self.creation_times[cache_key]
-                del self.file_counts[cache_key]
                 removed_count += 1
                 logger.info(f"清理过期的助手实例缓存: {cache_key}")
             except KeyError:
@@ -73,8 +71,7 @@ class FileLoadedAgentManager:
             logger.info(f"已清理 {removed_count} 个过期的助手实例缓存")
     
     async def get_or_create_agent(self, 
-                                 zip_url: str, 
-                                 files: List[str],
+                                 unique_id: str, 
                                  project_dir: str,
                                  model_name: str = "qwen3-next",
                                  api_key: Optional[str] = None,
@@ -83,7 +80,7 @@ class FileLoadedAgentManager:
         """获取或创建文件预加载的助手实例
         
         Args:
-            zip_url: ZIP 文件的 URL
+            unique_id: 项目的唯一标识符
             files: 需要预加载的文件路径列表
             project_dir: 项目目录路径，用于读取system_prompt.md和mcp_settings.json
             model_name: 模型名称
@@ -97,12 +94,16 @@ class FileLoadedAgentManager:
         import os
         import json
         
-        # 从项目目录读取system_prompt.md和mcp_settings.json
+        # 读取system_prompt：优先从项目目录读取，然后降级到全局配置
+                   # 降级到全局配置
         system_prompt_template = ""
-        system_prompt_path = os.path.join(project_dir, "system_prompt.md")
-        if os.path.exists(system_prompt_path):
-            with open(system_prompt_path, "r", encoding="utf-8") as f:
-                system_prompt_template = f.read().strip()
+        # 尝试从项目目录读取
+        system_prompt_file = os.path.join(project_dir, "system_prompt.md")
+        if not os.path.exists(system_prompt_file):
+            system_prompt_file = "./system_prompt.md"
+
+        with open(system_prompt_file, "r", encoding="utf-8") as f:
+            system_prompt_template = f.read().strip()
         
         readme = ""
         readme_path = os.path.join(project_dir, "README.md")
@@ -110,55 +111,69 @@ class FileLoadedAgentManager:
             with open(readme_path, "r", encoding="utf-8") as f:
                 readme = f.read().strip()
         dataset_dir = os.path.join(project_dir, "dataset")
- 
-        system_prompt = system_prompt_template.replace("{dataset_dir}", str(dataset_dir)).replace("{readme}", str(readme))
+
+        final_system_prompt = system_prompt_template.replace("{dataset_dir}", str(dataset_dir)).replace("{readme}", str(readme))
+        logger.info(f"Loaded global system_prompt for unique_id: {unique_id}")
+        if not final_system_prompt:
+            logger.info(f"No system_prompt found for unique_id: {unique_id}")
         
-        mcp_settings = {}
-        mcp_settings_path = os.path.join(project_dir, "mcp_settings.json")
-        if os.path.exists(mcp_settings_path):
-            with open(mcp_settings_path, "r", encoding="utf-8") as f:
-                mcp_settings = json.load(f)
+        # 读取mcp_settings：优先从项目目录读取，然后降级到全局配置
+        final_mcp_settings = None
         
-        cache_key = self._get_zip_url_hash(zip_url)
+        # 尝试从项目目录读取
+        mcp_settings_file = os.path.join(project_dir, "mcp_settings.json")
+        if os.path.exists(mcp_settings_file):
+            with open(mcp_settings_file, 'r', encoding='utf-8') as f:
+                final_mcp_settings = json.load(f)
+            logger.info(f"Loaded mcp_settings from project directory for unique_id: {unique_id}")
+        else:
+            # 降级到全局配置
+            mcp_settings_path = "./mcp/mcp_settings.json"
+            if os.path.exists(mcp_settings_path):
+                with open(mcp_settings_path, "r", encoding="utf-8") as f:
+                    final_mcp_settings = json.load(f)
+                logger.info(f"Loaded global mcp_settings for unique_id: {unique_id}")
+            else:
+                final_mcp_settings = []
+                logger.info(f"No mcp_settings found for unique_id: {unique_id}")
+        
+        if final_mcp_settings is None:
+            final_mcp_settings = []
+        
+        cache_key = self._get_cache_key(unique_id)
         
         # 检查是否已存在该助手实例
         if cache_key in self.agents:
             self._update_access_time(cache_key)
             agent = self.agents[cache_key]
             
-            # 动态更新 LLM 配置（如果参数有变化）
-            update_agent_llm(agent, model_name, api_key, model_server, generate_cfg)
+            # 动态更新 LLM 配置和系统设置（如果参数有变化）
+            update_agent_llm(agent, model_name, api_key, model_server, generate_cfg, final_system_prompt, final_mcp_settings)
             
-            # 如果从项目目录读取到了system_prompt，更新agent的系统消息
-            if system_prompt:
-                agent.system_message = system_prompt
-            
-            logger.info(f"复用现有的助手实例缓存: {cache_key} (文件数: {len(files)})")
+            logger.info(f"复用现有的助手实例缓存: {cache_key} (unique_id: {unique_id}")
             return agent
         
         # 清理过期实例
         self._cleanup_old_agents()
         
         # 创建新的助手实例，预加载文件
-        logger.info(f"创建新的助手实例缓存: {cache_key}, 预加载文件数: {len(files)}")
+        logger.info(f"创建新的助手实例缓存: {cache_key}, unique_id: {unique_id}")
         current_time = time.time()
         
         agent = init_agent_service_with_files(
-            files=files, 
             model_name=model_name, 
             api_key=api_key, 
             model_server=model_server, 
             generate_cfg=generate_cfg,
-            system_prompt=system_prompt,
-            mcp=mcp_settings
+            system_prompt=final_system_prompt,
+            mcp=final_mcp_settings
         )
         
         # 缓存实例
         self.agents[cache_key] = agent
-        self.zip_urls[cache_key] = zip_url
+        self.unique_ids[cache_key] = unique_id
         self.access_times[cache_key] = current_time
         self.creation_times[cache_key] = current_time
-        self.file_counts[cache_key] = len(files)
         
         logger.info(f"助手实例缓存创建完成: {cache_key}")
         return agent
@@ -174,8 +189,7 @@ class FileLoadedAgentManager:
         
         for cache_key, agent in self.agents.items():
             stats["agents"][cache_key] = {
-                "zip_url": self.zip_urls.get(cache_key, "unknown"),
-                "file_count": self.file_counts.get(cache_key, 0),
+                "unique_id": self.unique_ids.get(cache_key, "unknown"),
                 "created_at": self.creation_times.get(cache_key, 0),
                 "last_accessed": self.access_times.get(cache_key, 0),
                 "age_seconds": int(current_time - self.creation_times.get(cache_key, current_time)),
@@ -193,40 +207,34 @@ class FileLoadedAgentManager:
         cache_count = len(self.agents)
         
         self.agents.clear()
-        self.zip_urls.clear()
+        self.unique_ids.clear()
         self.access_times.clear()
         self.creation_times.clear()
-        self.file_counts.clear()
         
         logger.info(f"已清空所有助手实例缓存，共清理 {cache_count} 个实例")
         return cache_count
     
-    def remove_cache_by_url(self, zip_url: str) -> bool:
-        """根据 ZIP URL 移除特定的缓存
+    def remove_cache_by_unique_id(self, unique_id: str) -> bool:
+        """根据 unique_id 移除特定的缓存
         
         Args:
-            zip_url: ZIP 文件 URL
+            unique_id: 项目的唯一标识符
             
         Returns:
             bool: 是否成功移除
         """
-        cache_key = self._get_zip_url_hash(zip_url)
+        cache_key = self._get_cache_key(unique_id)
         
         if cache_key in self.agents:
             del self.agents[cache_key]
-            del self.zip_urls[cache_key]
+            del self.unique_ids[cache_key]
             del self.access_times[cache_key]
             del self.creation_times[cache_key]
-            del self.file_counts[cache_key]
             
-            logger.info(f"已移除特定 ZIP URL 的助手实例缓存: {zip_url}")
+            logger.info(f"已移除特定 unique_id 的助手实例缓存: {unique_id}")
             return True
         
         return False
-    
-    def list_cached_zip_urls(self) -> List[str]:
-        """列出所有缓存的 ZIP URL"""
-        return list(self.zip_urls.values())
 
 
 # 全局文件预加载助手管理器实例
diff --git a/gbase_agent.py b/gbase_agent.py
index dd0de33..6740722 100644
--- a/gbase_agent.py
+++ b/gbase_agent.py
@@ -103,7 +103,7 @@ def init_agent_service_universal():
     return init_agent_service_with_files(files=None)
 
 
-def init_agent_service_with_files(files: Optional[List[str]] = None, rag_cfg: Optional[Dict] = None, 
+def init_agent_service_with_files(rag_cfg: Optional[Dict] = None, 
                                   model_name: str = "qwen3-next", api_key: Optional[str] = None, 
                                   model_server: Optional[str] = None, generate_cfg: Optional[Dict] = None,
                                   system_prompt: Optional[str] = None, mcp: Optional[List[Dict]] = None):
@@ -160,8 +160,8 @@ def init_agent_service_with_files(files: Optional[List[str]] = None, rag_cfg: Op
     return bot
 
 
-def update_agent_llm(agent, model_name: str, api_key: str = None, model_server: str = None,generate_cfg: Dict = None):
-    """动态更新助手实例的LLM，支持从接口传入参数"""
+def update_agent_llm(agent, model_name: str, api_key: str = None, model_server: str = None, generate_cfg: Dict = None, system_prompt: str = None, mcp_settings: List[Dict] = None):
+    """动态更新助手实例的LLM和配置，支持从接口传入参数"""
 
     # 获取基础配置
     llm_config =  {
@@ -181,6 +181,14 @@ def update_agent_llm(agent, model_name: str, api_key: str = None, model_server:
     # 动态设置LLM
     agent.llm = llm_instance
     
+    # 更新系统消息（如果提供）
+    if system_prompt:
+        agent.system_message = system_prompt
+    
+    # 更新MCP设置（如果提供）
+    if mcp_settings:
+        agent.function_list = mcp_settings
+    
     return agent
 
 
diff --git a/mcp/mcp_settings.json b/mcp/mcp_settings.json
index aa319d9..7cb1a07 100644
--- a/mcp/mcp_settings.json
+++ b/mcp/mcp_settings.json
@@ -5,10 +5,10 @@
         "command": "mcp-ripgrep",
         "args": []
       },
-      "json-reader": {
+      "semantic_search": {
         "command": "python",
         "args": [
-          "./mcp/json_reader_server.py"
+          "./mcp/semantic_search_server.py"
         ]
       },
       "multi-keyword-search": {
diff --git a/mcp/multi_keyword_search_server.py b/mcp/multi_keyword_search_server.py
index 616a6c4..c45eb9f 100644
--- a/mcp/multi_keyword_search_server.py
+++ b/mcp/multi_keyword_search_server.py
@@ -125,13 +125,20 @@ def multi_keyword_search(keywords: List[str], file_paths: List[str],
         try:
             # 解析相对路径
             if not os.path.isabs(file_path):
+                # 移除 projects/ 前缀（如果存在）
+                clean_path = file_path
+                if clean_path.startswith('projects/'):
+                    clean_path = clean_path[9:]  # 移除 'projects/' 前缀
+                elif clean_path.startswith('./projects/'):
+                    clean_path = clean_path[11:]  # 移除 './projects/' 前缀
+                
                 # 尝试在项目目录中查找文件
-                full_path = os.path.join(project_data_dir, file_path.lstrip('./'))
+                full_path = os.path.join(project_data_dir, clean_path.lstrip('./'))
                 if os.path.exists(full_path):
                     valid_paths.append(full_path)
                 else:
                     # 如果直接路径不存在，尝试递归查找
-                    found = find_file_in_project(file_path, project_data_dir)
+                    found = find_file_in_project(clean_path, project_data_dir)
                     if found:
                         valid_paths.append(found)
             else:
diff --git a/mcp/semantic_search_server.py b/mcp/semantic_search_server.py
index ef90174..64ca075 100644
--- a/mcp/semantic_search_server.py
+++ b/mcp/semantic_search_server.py
@@ -87,11 +87,18 @@ def semantic_search(query: str, embeddings_file: str, top_k: int = 20) -> Dict[s
     try:
         # 解析相对路径
         if not os.path.isabs(embeddings_file):
+            # 移除 projects/ 前缀（如果存在）
+            clean_path = embeddings_file
+            if clean_path.startswith('projects/'):
+                clean_path = clean_path[9:]  # 移除 'projects/' 前缀
+            elif clean_path.startswith('./projects/'):
+                clean_path = clean_path[11:]  # 移除 './projects/' 前缀
+            
             # 尝试在项目目录中查找文件
-            full_path = os.path.join(project_data_dir, embeddings_file.lstrip('./'))
+            full_path = os.path.join(project_data_dir, clean_path.lstrip('./'))
             if not os.path.exists(full_path):
                 # 如果直接路径不存在，尝试递归查找
-                found = find_file_in_project(embeddings_file, project_data_dir)
+                found = find_file_in_project(clean_path, project_data_dir)
                 if found:
                     embeddings_file = found
                 else:
diff --git a/organize_dataset_files.py b/organize_dataset_files.py
new file mode 100644
index 0000000..638492b
--- /dev/null
+++ b/organize_dataset_files.py
@@ -0,0 +1,182 @@
+#!/usr/bin/env python3
+import os
+import shutil
+from pathlib import Path
+
+def is_file_already_processed(target_file: Path, pagination_file: Path, embeddings_file: Path) -> bool:
+    """Check if a file has already been processed (document.txt, pagination.txt, and embeddings exist)"""
+    if not target_file.exists():
+        return False
+    
+    # Check if pagination and embeddings files exist and are not empty
+    if pagination_file.exists() and embeddings_file.exists():
+        # Check file sizes to ensure they're not empty
+        if pagination_file.stat().st_size > 0 and embeddings_file.stat().st_size > 0:
+            return True
+    
+    return False
+
+def organize_single_project_files(unique_id: str, skip_processed=True):
+    """Organize files for a single project from projects/{unique_id}/files to projects/{unique_id}/dataset/{file_name}/document.txt"""
+    
+    project_dir = Path("projects") / unique_id
+    
+    if not project_dir.exists():
+        print(f"Project directory not found: {project_dir}")
+        return
+    
+    print(f"Organizing files for project: {unique_id} (skip_processed={skip_processed})")
+    
+    files_dir = project_dir / "files"
+    dataset_dir = project_dir / "dataset"
+    
+    # Check if files directory exists and has files
+    if not files_dir.exists():
+        print(f"  No files directory found, skipping...")
+        return
+        
+    files = list(files_dir.glob("*"))
+    if not files:
+        print(f"  Files directory is empty, skipping...")
+        return
+        
+    # Create dataset directory if it doesn't exist
+    dataset_dir.mkdir(exist_ok=True)
+    
+    # Copy each file to its own directory
+    for file_path in files:
+        if file_path.is_file():
+            # Get filename without extension as directory name
+            file_name_without_ext = file_path.stem
+            target_dir = dataset_dir / file_name_without_ext
+            target_file = target_dir / "document.txt"
+            pagination_file = target_dir / "pagination.txt"
+            embeddings_file = target_dir / "document_embeddings.pkl"
+            
+            # Check if file is already processed
+            if skip_processed and is_file_already_processed(target_file, pagination_file, embeddings_file):
+                print(f"  Skipping already processed file: {file_path.name}")
+                continue
+            
+            print(f"  Copying {file_path.name} -> {target_file.relative_to(project_dir)}")
+            
+            # Create target directory
+            target_dir.mkdir(exist_ok=True)
+            
+            # Copy and rename file
+            shutil.copy2(str(file_path), str(target_file))
+            
+    print(f"  Files remain in original location (copied to dataset structure)")
+    
+    # Process each document.txt file: split pages and generate embeddings
+    if not skip_processed:
+        import sys
+        sys.path.append(os.path.join(os.path.dirname(__file__), 'embedding'))
+        
+        from embedding import split_document_by_pages, embed_document
+        
+        for file_path in files:
+            if file_path.is_file():
+                file_name_without_ext = file_path.stem
+                target_dir = dataset_dir / file_name_without_ext
+                document_file = target_dir / "document.txt"
+                pagination_file = target_dir / "pagination.txt"
+                embeddings_file = target_dir / "document_embeddings.pkl"
+                
+                # Skip if already processed
+                if is_file_already_processed(document_file, pagination_file, embeddings_file):
+                    print(f"  Skipping document processing for already processed file: {file_path.name}")
+                    continue
+                
+                # Split document by pages
+                print(f"  Splitting pages for {document_file.name}")
+                try:
+                    pages = split_document_by_pages(str(document_file), str(pagination_file))
+                    print(f"    Generated {len(pages)} pages")
+                except Exception as e:
+                    print(f"    Failed to split pages: {e}")
+                    continue
+                
+                # Generate embeddings
+                print(f"  Generating embeddings for {document_file.name}")
+                try:
+                    # Set local model path for faster processing
+                    local_model_path = "./models/paraphrase-multilingual-MiniLM-L12-v2"
+                    if not os.path.exists(local_model_path):
+                        local_model_path = None  # Fallback to HuggingFace model
+                    
+                    embedding_data = embed_document(
+                        str(document_file), 
+                        str(embeddings_file),
+                        chunking_strategy='smart',
+                        model_path=local_model_path,
+                        max_chunk_size=800,
+                        overlap=100
+                    )
+                    
+                    if embedding_data:
+                        print(f"    Generated embeddings for {len(embedding_data['chunks'])} chunks")
+                    else:
+                        print(f"    Failed to generate embeddings")
+                except Exception as e:
+                    print(f"    Failed to generate embeddings: {e}")
+        
+        print(f"  Document processing completed for project {unique_id}")
+    else:
+        print(f"  Skipping document processing (skip_processed=True)")
+
+
+def organize_dataset_files():
+    """Move files from projects/{unique_id}/files to projects/{unique_id}/dataset/{file_name}/document.txt"""
+    
+    projects_dir = Path("projects")
+    
+    if not projects_dir.exists():
+        print("Projects directory not found")
+        return
+    
+    # Get all project directories (exclude cache and other non-project dirs)
+    project_dirs = [d for d in projects_dir.iterdir() 
+                   if d.is_dir() and d.name != "_cache" and not d.name.startswith(".")]
+    
+    for project_dir in project_dirs:
+        print(f"\nProcessing project: {project_dir.name}")
+        
+        files_dir = project_dir / "files"
+        dataset_dir = project_dir / "dataset"
+        
+        # Check if files directory exists and has files
+        if not files_dir.exists():
+            print(f"  No files directory found, skipping...")
+            continue
+            
+        files = list(files_dir.glob("*"))
+        if not files:
+            print(f"  Files directory is empty, skipping...")
+            continue
+            
+        # Create dataset directory if it doesn't exist
+        dataset_dir.mkdir(exist_ok=True)
+        
+        # Move each file to its own directory
+        for file_path in files:
+            if file_path.is_file():
+                # Get filename without extension as directory name
+                file_name_without_ext = file_path.stem
+                target_dir = dataset_dir / file_name_without_ext
+                target_file = target_dir / "document.txt"
+                
+                print(f"  Copying {file_path.name} -> {target_file.relative_to(project_dir)}")
+                
+                # Create target directory
+                target_dir.mkdir(exist_ok=True)
+                
+                # Copy and rename file
+                shutil.copy2(str(file_path), str(target_file))
+                
+        print(f"  Files remain in original location (copied to dataset structure)")
+    
+    print("\nFile organization complete!")
+
+if __name__ == "__main__":
+    organize_dataset_files()
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index b667448..9b248e6 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,17 @@
 # This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
+[[package]]
+name = "aiofiles"
+version = "25.1.0"
+description = "File support for asyncio."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "aiofiles-25.1.0-py3-none-any.whl", hash = "sha256:abe311e527c862958650f9438e859c1fa7568a141b22abcd015e120e86a85695"},
+    {file = "aiofiles-25.1.0.tar.gz", hash = "sha256:a8d728f0a29de45dc521f18f07297428d56992a742f0cd2701ba86e44d23d5b2"},
+]
+
 [[package]]
 name = "aiohappyeyeballs"
 version = "2.6.1"
@@ -3949,4 +3961,4 @@ propcache = ">=0.2.1"
 [metadata]
 lock-version = "2.1"
 python-versions = "3.12.0"
-content-hash = "e3237e20c799a13a0854f786a34a7c7cb2d5020902281c92ebff2e497492edd1"
+content-hash = "06c3b78c8107692eb5944b144ae4df02862fa5e4e8a198f6ccfa07c6743a49cf"
diff --git a/pyproject.toml b/pyproject.toml
index f48a15b..a6d4049 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,8 @@ dependencies = [
     "transformers",
     "sentence-transformers",
     "numpy<2",
+    "aiohttp",
+    "aiofiles",
 ]
 
 
diff --git a/unique_map.json b/unique_map.json
deleted file mode 100644
index 88438e9..0000000
--- a/unique_map.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "b743ccc3-13be-43ea-8ec9-4ce9c86103b3": [
-    "public/all_hp_product_spec_book2506.txt"
-  ]
-}