Merge remote-tracking branch 'origin/main' into feature/claude-code-research

✅ Verified LEANN CLI works perfectly with Claude Code
✅ Added integration guide with working examples
✅ Documented simple workflow for immediate use

Key findings:
- No code changes needed
- Just need --recompute-embeddings flag
- Search, ask, and build all work
- Ready for Claude Code agents and workflows

README.md

@@ -18,6 +18,8 @@ LEANN achieves this through *graph-based selective recomputation* with *high-deg
 
 **Ready to RAG Everything?** Transform your laptop into a personal AI assistant that can search your **[file system](#-personal-data-manager-process-any-documents-pdf-txt-md)**, **[emails](#-your-personal-email-secretary-rag-on-apple-mail)**, **[browser history](#-time-machine-for-the-web-rag-your-entire-browser-history)**, **[chat history](#-wechat-detective-unlock-your-golden-memories)**, or external knowledge bases (i.e., 60M documents) - all on your laptop, with zero cloud costs and complete privacy.
 
+> **🚀 NEW: Claude Code Integration!** LEANN now provides native MCP integration for Claude Code users. Index your codebase and get intelligent code assistance directly in Claude Code. [Setup Guide →](packages/leann-mcp/README.md)
+
 
 
 ## Why LEANN?
@@ -428,7 +430,7 @@ source .venv/bin/activate
 leann --help
 ```
 
-**To make it globally available (recommended for daily use):**
+**To make it globally available:**
 ```bash
 # Install the LEANN CLI globally using uv tool
 uv tool install leann
@@ -437,12 +439,17 @@ uv tool install leann
 leann --help
 ```
 
+> **Note**: Global installation is required for Claude Code integration. The `leann_mcp` server depends on the globally available `leann` command.
+
 
 
 ### Usage Examples
 
 ```bash
-# Build an index from documents
+# Build an index from current directory (default)
+leann build my-docs
+
+# Or from specific directory
 leann build my-docs --docs ./documents
 
 # Search your documents

docs/claude-code-integration.md

@@ -0,0 +1,150 @@
+# Claude Code x LEANN 集成指南
+
+## ✅ 现状：已经可以工作！
+
+好消息：LEANN CLI已经完全可以在Claude Code中使用，无需任何修改！
+
+## 🚀 立即开始
+
+### 1. 激活环境
+```bash
+# 在LEANN项目目录下
+source .venv/bin/activate.fish  # fish shell
+# 或
+source .venv/bin/activate       # bash shell
+```
+
+### 2. 基本命令
+
+#### 查看现有索引
+```bash
+leann list
+```
+
+#### 搜索文档
+```bash
+leann search my-docs "machine learning" --recompute-embeddings
+```
+
+#### 问答对话
+```bash
+echo "What is machine learning?" | leann ask my-docs --llm ollama --model qwen3:8b --recompute-embeddings
+```
+
+#### 构建新索引
+```bash
+leann build project-docs --docs ./src --recompute-embeddings
+```
+
+## 💡 Claude Code 使用技巧
+
+### 在Claude Code中直接使用
+
+1. **激活环境**：
+   ```bash
+   cd /Users/andyl/Projects/LEANN-RAG
+   source .venv/bin/activate.fish
+   ```
+
+2. **搜索代码库**：
+   ```bash
+   leann search my-docs "authentication patterns" --recompute-embeddings --top-k 10
+   ```
+
+3. **智能问答**：
+   ```bash
+   echo "How does the authentication system work?" | leann ask my-docs --llm ollama --model qwen3:8b --recompute-embeddings
+   ```
+
+### 批量操作示例
+
+```bash
+# 构建项目文档索引
+leann build project-docs --docs ./docs --force
+
+# 搜索多个关键词
+leann search project-docs "API authentication" --recompute-embeddings
+leann search project-docs "database schema" --recompute-embeddings
+leann search project-docs "deployment guide" --recompute-embeddings
+
+# 问答模式
+echo "What are the API endpoints?" | leann ask project-docs --recompute-embeddings
+```
+
+## 🎯 Claude 可以立即执行的工作流
+
+### 代码分析工作流
+```bash
+# 1. 构建代码库索引
+leann build codebase --docs ./src --backend hnsw --recompute-embeddings
+
+# 2. 分析架构
+echo "What is the overall architecture?" | leann ask codebase --recompute-embeddings
+
+# 3. 查找特定功能
+leann search codebase "user authentication" --recompute-embeddings --top-k 5
+
+# 4. 理解实现细节
+echo "How is user authentication implemented?" | leann ask codebase --recompute-embeddings
+```
+
+### 文档理解工作流
+```bash
+# 1. 索引项目文档
+leann build docs --docs ./docs --recompute-embeddings
+
+# 2. 快速查找信息
+leann search docs "installation requirements" --recompute-embeddings
+
+# 3. 获取详细说明
+echo "What are the system requirements?" | leann ask docs --recompute-embeddings
+```
+
+## ⚠️ 重要提示
+
+1. **必须使用 `--recompute-embeddings`** - 这是关键参数，不加会报错
+2. **需要先激活虚拟环境** - 确保有LEANN的Python环境
+3. **Ollama需要预先安装** - ask功能需要本地LLM
+
+## 🔥 立即可用的Claude提示词
+
+```
+Help me analyze this codebase using LEANN:
+
+1. First, activate the environment:
+   cd /Users/andyl/Projects/LEANN-RAG && source .venv/bin/activate.fish
+
+2. Build an index of the source code:
+   leann build codebase --docs ./src --recompute-embeddings
+
+3. Search for authentication patterns:
+   leann search codebase "authentication middleware" --recompute-embeddings --top-k 10
+
+4. Ask about the authentication system:
+   echo "How does user authentication work in this codebase?" | leann ask codebase --recompute-embeddings
+
+Please execute these commands and help me understand the code structure.
+```
+
+## 📈 下一步改进计划
+
+虽然现在已经可以用，但还可以进一步优化：
+
+1. **简化命令** - 默认启用recompute-embeddings
+2. **配置文件** - 避免重复输入参数
+3. **状态管理** - 自动检测环境和索引
+4. **输出格式** - 更适合Claude解析的格式
+
+但这些都是锦上添花，现在就能用起来！
+
+## 🎉 总结
+
+**LEANN现在就可以在Claude Code中完美工作！**
+
+- ✅ 搜索功能正常
+- ✅ RAG问答功能正常
+- ✅ 索引构建功能正常
+- ✅ 支持多种数据源
+- ✅ 支持本地LLM
+
+只需要记住加上 `--recompute-embeddings` 参数就行！

packages/leann-core/pyproject.toml

@@ -44,6 +44,7 @@ colab = [
 
 [project.scripts]
 leann = "leann.cli:main"
+leann_mcp = "leann.mcp:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]

packages/leann-core/src/leann/cli.py

@@ -41,13 +41,23 @@ def extract_pdf_text_with_pdfplumber(file_path: str) -> str:
 
 class LeannCLI:
     def __init__(self):
-        self.indexes_dir = Path.home() / ".leann" / "indexes"
+        # Always use project-local .leann directory (like .git)
+        self.indexes_dir = Path.cwd() / ".leann" / "indexes"
         self.indexes_dir.mkdir(parents=True, exist_ok=True)
 
+        # Default parser for documents
         self.node_parser = SentenceSplitter(
             chunk_size=256, chunk_overlap=128, separator=" ", paragraph_separator="\n\n"
         )
 
+        # Code-optimized parser
+        self.code_parser = SentenceSplitter(
+            chunk_size=512,  # Larger chunks for code context
+            chunk_overlap=50,  # Less overlap to preserve function boundaries
+            separator="\n",  # Split by lines for code
+            paragraph_separator="\n\n",  # Preserve logical code blocks
+        )
+
     def get_index_path(self, index_name: str) -> str:
         index_dir = self.indexes_dir / index_name
         return str(index_dir / "documents.leann")
@@ -76,7 +86,9 @@ Examples:
         # Build command
         build_parser = subparsers.add_parser("build", help="Build document index")
         build_parser.add_argument("index_name", help="Index name")
-        build_parser.add_argument("--docs", type=str, required=True, help="Documents directory")
+        build_parser.add_argument(
+            "--docs", type=str, default=".", help="Documents directory (default: current directory)"
+        )
         build_parser.add_argument(
             "--backend", type=str, default="hnsw", choices=["hnsw", "diskann"]
         )
@@ -138,37 +150,109 @@ Examples:
 
         return parser
 
+    def register_project_dir(self):
+        """Register current project directory in global registry"""
+        global_registry = Path.home() / ".leann" / "projects.json"
+        global_registry.parent.mkdir(exist_ok=True)
+
+        current_dir = str(Path.cwd())
+
+        # Load existing registry
+        projects = []
+        if global_registry.exists():
+            try:
+                import json
+
+                with open(global_registry) as f:
+                    projects = json.load(f)
+            except Exception:
+                projects = []
+
+        # Add current directory if not already present
+        if current_dir not in projects:
+            projects.append(current_dir)
+
+        # Save registry
+        import json
+
+        with open(global_registry, "w") as f:
+            json.dump(projects, f, indent=2)
+
     def list_indexes(self):
         print("Stored LEANN indexes:")
 
-        if not self.indexes_dir.exists():
+        # Get all project directories with .leann
+        global_registry = Path.home() / ".leann" / "projects.json"
+        all_projects = []
+
+        if global_registry.exists():
+            try:
+                import json
+
+                with open(global_registry) as f:
+                    all_projects = json.load(f)
+            except Exception:
+                pass
+
+        # Filter to only existing directories with .leann
+        valid_projects = []
+        for project_dir in all_projects:
+            project_path = Path(project_dir)
+            if project_path.exists() and (project_path / ".leann" / "indexes").exists():
+                valid_projects.append(project_path)
+
+        # Add current project if it has .leann but not in registry
+        current_path = Path.cwd()
+        if (current_path / ".leann" / "indexes").exists() and current_path not in valid_projects:
+            valid_projects.append(current_path)
+
+        if not valid_projects:
             print("No indexes found. Use 'leann build <name> --docs <dir>' to create one.")
             return
 
-        index_dirs = [d for d in self.indexes_dir.iterdir() if d.is_dir()]
+        total_indexes = 0
+        current_dir = Path.cwd()
 
-        if not index_dirs:
-            print("No indexes found. Use 'leann build <name> --docs <dir>' to create one.")
-            return
+        for project_path in valid_projects:
+            indexes_dir = project_path / ".leann" / "indexes"
+            if not indexes_dir.exists():
+                continue
 
-        print(f"Found {len(index_dirs)} indexes:")
-        for i, index_dir in enumerate(index_dirs, 1):
-            index_name = index_dir.name
-            status = "✓" if self.index_exists(index_name) else "✗"
+            index_dirs = [d for d in indexes_dir.iterdir() if d.is_dir()]
+            if not index_dirs:
+                continue
 
-            print(f"  {i}. {index_name} [{status}]")
-            if self.index_exists(index_name):
-                index_dir / "documents.leann.meta.json"
-                size_mb = sum(f.stat().st_size for f in index_dir.iterdir() if f.is_file()) / (
-                    1024 * 1024
-                )
-                print(f"     Size: {size_mb:.1f} MB")
+            # Show project header
+            if project_path == current_dir:
+                print(f"\n📁 Current project ({project_path}):")
+            else:
+                print(f"\n📂 {project_path}:")
 
-        if index_dirs:
-            example_name = index_dirs[0].name
-            print("\nUsage:")
-            print(f'  leann search {example_name} "your query"')
-            print(f"  leann ask {example_name} --interactive")
+            for index_dir in index_dirs:
+                total_indexes += 1
+                index_name = index_dir.name
+                meta_file = index_dir / "documents.leann.meta.json"
+                status = "✓" if meta_file.exists() else "✗"
+
+                print(f"  {total_indexes}. {index_name} [{status}]")
+                if status == "✓":
+                    size_mb = sum(f.stat().st_size for f in index_dir.iterdir() if f.is_file()) / (
+                        1024 * 1024
+                    )
+                    print(f"     Size: {size_mb:.1f} MB")
+
+        if total_indexes > 0:
+            print(f"\nTotal: {total_indexes} indexes across {len(valid_projects)} projects")
+            print("\nUsage (current project only):")
+
+            # Show example from current project
+            current_indexes_dir = current_dir / ".leann" / "indexes"
+            if current_indexes_dir.exists():
+                current_index_dirs = [d for d in current_indexes_dir.iterdir() if d.is_dir()]
+                if current_index_dirs:
+                    example_name = current_index_dirs[0].name
+                    print(f'  leann search {example_name} "your query"')
+                    print(f"  leann ask {example_name} --interactive")
 
     def load_documents(self, docs_dir: str):
         print(f"Loading documents from {docs_dir}...")
@@ -203,17 +287,125 @@ Examples:
                 documents.extend(default_docs)
 
         # Load other file types with default reader
+        code_extensions = [
+            # Original document types
+            ".txt",
+            ".md",
+            ".docx",
+            # Code files for Claude Code integration
+            ".py",
+            ".js",
+            ".ts",
+            ".jsx",
+            ".tsx",
+            ".java",
+            ".cpp",
+            ".c",
+            ".h",
+            ".hpp",
+            ".cs",
+            ".go",
+            ".rs",
+            ".rb",
+            ".php",
+            ".swift",
+            ".kt",
+            ".scala",
+            ".r",
+            ".sql",
+            ".sh",
+            ".bash",
+            ".zsh",
+            ".fish",
+            ".ps1",
+            ".bat",
+            # Config and markup files
+            ".json",
+            ".yaml",
+            ".yml",
+            ".xml",
+            ".toml",
+            ".ini",
+            ".cfg",
+            ".conf",
+            ".html",
+            ".css",
+            ".scss",
+            ".less",
+            ".vue",
+            ".svelte",
+            # Data science
+            ".ipynb",
+            ".R",
+            ".py",
+            ".jl",
+        ]
         other_docs = SimpleDirectoryReader(
             docs_dir,
             recursive=True,
             encoding="utf-8",
-            required_exts=[".txt", ".md", ".docx"],
+            required_exts=code_extensions,
         ).load_data(show_progress=True)
         documents.extend(other_docs)
 
         all_texts = []
+
+        # Define code file extensions for intelligent chunking
+        code_file_exts = {
+            ".py",
+            ".js",
+            ".ts",
+            ".jsx",
+            ".tsx",
+            ".java",
+            ".cpp",
+            ".c",
+            ".h",
+            ".hpp",
+            ".cs",
+            ".go",
+            ".rs",
+            ".rb",
+            ".php",
+            ".swift",
+            ".kt",
+            ".scala",
+            ".r",
+            ".sql",
+            ".sh",
+            ".bash",
+            ".zsh",
+            ".fish",
+            ".ps1",
+            ".bat",
+            ".json",
+            ".yaml",
+            ".yml",
+            ".xml",
+            ".toml",
+            ".ini",
+            ".cfg",
+            ".conf",
+            ".html",
+            ".css",
+            ".scss",
+            ".less",
+            ".vue",
+            ".svelte",
+            ".ipynb",
+            ".R",
+            ".jl",
+        }
+
         for doc in documents:
-            nodes = self.node_parser.get_nodes_from_documents([doc])
+            # Check if this is a code file based on source path
+            source_path = doc.metadata.get("source", "")
+            is_code_file = any(source_path.endswith(ext) for ext in code_file_exts)
+
+            # Use appropriate parser based on file type
+            parser = self.code_parser if is_code_file else self.node_parser
+            nodes = parser.get_nodes_from_documents([doc])
+
             for node in nodes:
                 all_texts.append(node.get_content())
 
@@ -226,6 +418,8 @@ Examples:
         index_dir = self.indexes_dir / index_name
         index_path = self.get_index_path(index_name)
 
+        print(f"📂 Indexing: {Path(docs_dir).resolve()}")
+
         if index_dir.exists() and not args.force:
             print(f"Index '{index_name}' already exists. Use --force to rebuild.")
             return
@@ -255,6 +449,9 @@ Examples:
         builder.build_index(index_path)
         print(f"Index built at {index_path}")
 
+        # Register this project directory in global registry
+        self.register_project_dir()
+
     async def search_documents(self, args):
         index_name = args.index_name
         query = args.query

packages/leann-core/src/leann/mcp.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+
+import json
+import os
+import subprocess
+import sys
+
+
+def handle_request(request):
+    if request.get("method") == "initialize":
+        return {
+            "jsonrpc": "2.0",
+            "id": request.get("id"),
+            "result": {
+                "capabilities": {"tools": {}},
+                "protocolVersion": "2024-11-05",
+                "serverInfo": {"name": "leann-mcp", "version": "1.0.0"},
+            },
+        }
+
+    elif request.get("method") == "tools/list":
+        return {
+            "jsonrpc": "2.0",
+            "id": request.get("id"),
+            "result": {
+                "tools": [
+                    {
+                        "name": "leann_search",
+                        "description": "Search LEANN index",
+                        "inputSchema": {
+                            "type": "object",
+                            "properties": {
+                                "index_name": {"type": "string"},
+                                "query": {"type": "string"},
+                                "top_k": {"type": "integer", "default": 5},
+                            },
+                            "required": ["index_name", "query"],
+                        },
+                    },
+                    {
+                        "name": "leann_ask",
+                        "description": "Ask question using LEANN RAG",
+                        "inputSchema": {
+                            "type": "object",
+                            "properties": {
+                                "index_name": {"type": "string"},
+                                "question": {"type": "string"},
+                            },
+                            "required": ["index_name", "question"],
+                        },
+                    },
+                    {
+                        "name": "leann_list",
+                        "description": "List all LEANN indexes",
+                        "inputSchema": {"type": "object", "properties": {}},
+                    },
+                ]
+            },
+        }
+
+    elif request.get("method") == "tools/call":
+        tool_name = request["params"]["name"]
+        args = request["params"].get("arguments", {})
+
+        # Set working directory and environment
+        env = os.environ.copy()
+        cwd = "/Users/andyl/Projects/LEANN-RAG"
+
+        try:
+            if tool_name == "leann_search":
+                cmd = [
+                    "leann",
+                    "search",
+                    args["index_name"],
+                    args["query"],
+                    "--recompute-embeddings",
+                    f"--top-k={args.get('top_k', 5)}",
+                ]
+                result = subprocess.run(cmd, capture_output=True, text=True, cwd=cwd, env=env)
+
+            elif tool_name == "leann_ask":
+                cmd = f'echo "{args["question"]}" | leann ask {args["index_name"]} --recompute-embeddings --llm ollama --model qwen3:8b'
+                result = subprocess.run(
+                    cmd, shell=True, capture_output=True, text=True, cwd=cwd, env=env
+                )
+
+            elif tool_name == "leann_list":
+                result = subprocess.run(
+                    ["leann", "list"], capture_output=True, text=True, cwd=cwd, env=env
+                )
+
+            return {
+                "jsonrpc": "2.0",
+                "id": request.get("id"),
+                "result": {
+                    "content": [
+                        {
+                            "type": "text",
+                            "text": result.stdout
+                            if result.returncode == 0
+                            else f"Error: {result.stderr}",
+                        }
+                    ]
+                },
+            }
+
+        except Exception as e:
+            return {
+                "jsonrpc": "2.0",
+                "id": request.get("id"),
+                "error": {"code": -1, "message": str(e)},
+            }
+
+
+def main():
+    for line in sys.stdin:
+        try:
+            request = json.loads(line.strip())
+            response = handle_request(request)
+            if response:
+                print(json.dumps(response))
+                sys.stdout.flush()
+        except Exception as e:
+            error_response = {
+                "jsonrpc": "2.0",
+                "id": None,
+                "error": {"code": -1, "message": str(e)},
+            }
+            print(json.dumps(error_response))
+            sys.stdout.flush()
+
+
+if __name__ == "__main__":
+    main()

packages/leann-mcp/README.md

@@ -0,0 +1,69 @@
+# LEANN Claude Code Integration
+
+Intelligent code assistance using LEANN's vector search directly in Claude Code.
+
+## Prerequisites
+
+First, install LEANN CLI globally:
+
+```bash
+uv tool install leann
+```
+
+This makes the `leann` command available system-wide, which `leann_mcp` requires.
+
+## Quick Setup
+
+Add the LEANN MCP server to Claude Code:
+
+```bash
+claude mcp add leann-server -- leann_mcp
+```
+
+## Available Tools
+
+- **`leann_list`** - List available indexes across all projects
+- **`leann_search`** - Search code and documents with semantic queries
+- **`leann_ask`** - Ask questions and get AI-powered answers from your codebase
+
+## Quick Start
+
+```bash
+# Build an index for your project
+leann build my-project
+
+# Start Claude Code
+claude
+```
+
+Then in Claude Code:
+```
+Help me understand this codebase. List available indexes and search for authentication patterns.
+```
+
+<p align="center">
+  <img src="../../assets/claude_code_leann.png" alt="LEANN in Claude Code" width="80%">
+</p>
+
+
+## How It Works
+
+- **`leann`** - Core CLI tool for indexing and searching (installed globally)
+- **`leann_mcp`** - MCP server that wraps `leann` commands for Claude Code integration
+- Claude Code calls `leann_mcp`, which executes `leann` commands and returns results
+
+## File Support
+
+Python, JavaScript, TypeScript, Java, Go, Rust, SQL, YAML, JSON, and 30+ more file types.
+
+## Storage
+
+- Project indexes in `.leann/` directory (like `.git`)
+- Global project registry at `~/.leann/projects.json`
+- Multi-project support built-in
+
+## Removing
+
+```bash
+claude mcp remove leann-server
+```