fix: Use uv venv for Arch Linux CI wheel installation

- Use astral-sh/setup-uv@v4 action for consistency with other jobs
- Create virtual environment with uv venv to bypass PEP 668 restrictions
- Install wheels using uv pip install for faster dependency resolution
- Maintain tool consistency across the entire CI pipeline

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

.gitattributes

@@ -1 +0,0 @@
-paper_plot/data/big_graph_degree_data.npz filter=lfs diff=lfs merge=lfs -text

.github/workflows/build-reusable.yml

@@ -87,7 +87,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: ${{ inputs.ref }}
           submodules: recursive
@@ -98,21 +98,23 @@ jobs:
           python-version: ${{ matrix.python }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
 
       - name: Install system dependencies (Ubuntu)
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
           sudo apt-get install -y libomp-dev libboost-all-dev protobuf-compiler libzmq3-dev \
-            pkg-config libopenblas-dev patchelf libabsl-dev libaio-dev libprotobuf-dev
+            pkg-config libabsl-dev libaio-dev libprotobuf-dev \
+            patchelf
 
           # Install Intel MKL for DiskANN
           wget -q https://registrationcenter-download.intel.com/akdlm/IRC_NAS/79153e0f-74d7-45af-b8c2-258941adf58a/intel-onemkl-2025.0.0.940.sh
           sudo sh intel-onemkl-2025.0.0.940.sh -a --components intel.oneapi.lin.mkl.devel --action install --eula accept -s
           source /opt/intel/oneapi/setvars.sh
           echo "MKLROOT=/opt/intel/oneapi/mkl/latest" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=/opt/intel/oneapi/mkl/latest/lib/intel64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64_lin" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/oneapi/mkl/latest/lib/intel64" >> $GITHUB_ENV
 
       - name: Install system dependencies (macOS)
         if: runner.os == 'macOS'
@@ -304,3 +306,53 @@ jobs:
         with:
           name: packages-${{ matrix.os }}-py${{ matrix.python }}
           path: packages/*/dist/
+
+
+  arch-smoke:
+    name: Arch Linux smoke test (install & import)
+    needs: build
+    runs-on: ubuntu-latest
+    container:
+      image: archlinux:latest
+
+    steps:
+      - name: Prepare system
+        run: |
+          pacman -Syu --noconfirm
+          pacman -S --noconfirm python python-pip gcc git zlib openssl
+
+      - name: Download ALL wheel artifacts from this run
+        uses: actions/download-artifact@v5
+        with:
+          # Don't specify name, download all artifacts
+          path: ./wheels
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Create virtual environment and install wheels
+        run: |
+          uv venv
+          source .venv/bin/activate || source .venv/Scripts/activate
+          uv pip install --find-links wheels leann-core
+          uv pip install --find-links wheels leann-backend-hnsw
+          uv pip install --find-links wheels leann-backend-diskann
+          uv pip install --find-links wheels leann
+
+      - name: Import & tiny runtime check
+        env:
+          OMP_NUM_THREADS: 1
+          MKL_NUM_THREADS: 1
+        run: |
+          source .venv/bin/activate || source .venv/Scripts/activate
+          python - <<'PY'
+          import leann
+          import leann_backend_hnsw as h
+          import leann_backend_diskann as d
+          from leann import LeannBuilder, LeannSearcher
+          b = LeannBuilder(backend_name="hnsw")
+          b.add_text("hello arch")
+          b.build_index("arch_demo.leann")
+          s = LeannSearcher("arch_demo.leann")
+          print("search:", s.search("hello", top_k=1))
+          PY

.github/workflows/link-check.yml

@@ -14,6 +14,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: lycheeverse/lychee-action@v2
         with:
-          args: --no-progress --insecure README.md docs/ apps/ examples/ benchmarks/
+          args: --no-progress --insecure --user-agent 'curl/7.68.0' README.md docs/ apps/ examples/ benchmarks/
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -18,6 +18,7 @@ demo/experiment_results/**/*.json
 *.eml
 *.emlx
 *.json
+!.vscode/*.json
 *.sh
 *.txt
 !CMakeLists.txt

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "charliermarsh.ruff",
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,22 @@
+{
+  "python.defaultInterpreterPath": ".venv/bin/python",
+  "python.terminal.activateEnvironment": true,
+  "[python]": {
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit",
+      "source.fixAll": "explicit"
+    },
+    "editor.insertSpaces": true,
+    "editor.tabSize": 4
+  },
+  "ruff.enable": true,
+  "files.watcherExclude": {
+    "**/.venv/**": true,
+    "**/__pycache__/**": true,
+    "**/*.egg-info/**": true,
+    "**/build/**": true,
+    "**/dist/**": true
+  }
+}

README.md

@@ -5,7 +5,7 @@
 <p align="center">
   <img src="https://img.shields.io/badge/Python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue.svg" alt="Python Versions">
   <img src="https://github.com/yichuan-w/LEANN/actions/workflows/build-and-publish.yml/badge.svg" alt="CI Status">
-  <img src="https://img.shields.io/badge/Platform-Ubuntu%20%7C%20macOS%20(ARM64%2FIntel)-lightgrey" alt="Platform">
+  <img src="https://img.shields.io/badge/Platform-Ubuntu%20%26%20Arch%20%26%20WSL%20%7C%20macOS%20(ARM64%2FIntel)-lightgrey" alt="Platform">
   <img src="https://img.shields.io/badge/License-MIT-green.svg" alt="MIT License">
   <img src="https://img.shields.io/badge/MCP-Native%20Integration-blue" alt="MCP Integration">
 </p>
@@ -31,7 +31,7 @@ LEANN achieves this through *graph-based selective recomputation* with *high-deg
   <img src="assets/effects.png" alt="LEANN vs Traditional Vector DB Storage Comparison" width="70%">
 </p>
 
-> **The numbers speak for themselves:** Index 60 million text chunks in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks for different applications below ↓](#storage-comparison)
+> **The numbers speak for themselves:** Index 60 million text chunks in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks for different applications below ↓](#-storage-comparison)
 
 
 🔒 **Privacy:** Your data never leaves your laptop. No OpenAI, no cloud, no "terms of service".
@@ -70,8 +70,8 @@ uv venv
 source .venv/bin/activate
 uv pip install leann
 ```
-
-> Low-resource? See “Low-resource setups” in the [Configuration Guide](docs/configuration-guide.md#low-resource-setups).
+<!--
+> Low-resource? See “Low-resource setups” in the [Configuration Guide](docs/configuration-guide.md#low-resource-setups). -->
 
 <details>
 <summary>
@@ -87,15 +87,60 @@ git submodule update --init --recursive
 ```
 
 **macOS:**
+
+Note: DiskANN requires MacOS 13.3 or later.
+
 ```bash
-brew install llvm libomp boost protobuf zeromq pkgconf
-CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ uv sync
+brew install libomp boost protobuf zeromq pkgconf
+uv sync --extra diskann
 ```
 
-**Linux:**
+**Linux (Ubuntu/Debian):**
+
+Note: On Ubuntu 20.04, you may need to build a newer Abseil and pin Protobuf (e.g., v3.20.x) for building DiskANN. See [Issue #30](https://github.com/yichuan-w/LEANN/issues/30) for a step-by-step note.
+
+You can manually install [Intel oneAPI MKL](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) instead of `libmkl-full-dev` for DiskANN. You can also use `libopenblas-dev` for building HNSW only, by removing `--extra diskann` in the command below.
+
 ```bash
-sudo apt-get install libomp-dev libboost-all-dev protobuf-compiler libabsl-dev libmkl-full-dev libaio-dev libzmq3-dev
-uv sync
+sudo apt-get update && sudo apt-get install -y \
+  libomp-dev libboost-all-dev protobuf-compiler libzmq3-dev \
+  pkg-config libabsl-dev libaio-dev libprotobuf-dev \
+  libmkl-full-dev
+
+uv sync --extra diskann
+```
+
+**Linux (Arch Linux):**
+
+```bash
+sudo pacman -Syu && sudo pacman -S --needed base-devel cmake pkgconf git gcc \
+  boost boost-libs protobuf abseil-cpp libaio zeromq
+
+# For MKL in DiskANN
+sudo pacman -S --needed base-devel git
+git clone https://aur.archlinux.org/paru-bin.git
+cd paru-bin && makepkg -si
+paru -S intel-oneapi-mkl intel-oneapi-compiler
+source /opt/intel/oneapi/setvars.sh
+
+uv sync --extra diskann
+```
+
+**Linux (RHEL / CentOS Stream / Oracle / Rocky / AlmaLinux):**
+
+See [Issue #50](https://github.com/yichuan-w/LEANN/issues/50) for more details.
+
+```bash
+sudo dnf groupinstall -y "Development Tools"
+sudo dnf install -y libomp-devel boost-devel protobuf-compiler protobuf-devel \
+  abseil-cpp-devel libaio-devel zeromq-devel pkgconf-pkg-config
+
+# For MKL in DiskANN
+sudo dnf install -y intel-oneapi-mkl intel-oneapi-mkl-devel \
+  intel-oneapi-openmp || sudo dnf install -y intel-oneapi-compiler
+source /opt/intel/oneapi/setvars.sh
+
+uv sync --extra diskann
 ```
 
 </details>
@@ -426,21 +471,21 @@ Once the index is built, you can ask questions like:
 **The future of code assistance is here.** Transform your development workflow with LEANN's native MCP integration for Claude Code. Index your entire codebase and get intelligent code assistance directly in your IDE.
 
 **Key features:**
-- 🔍 **Semantic code search** across your entire project
+- 🔍 **Semantic code search** across your entire project, fully local index and lightweight
 - 📚 **Context-aware assistance** for debugging and development
 - 🚀 **Zero-config setup** with automatic language detection
 
 ```bash
 # Install LEANN globally for MCP integration
-uv tool install leann-core
-
+uv tool install leann-core --with leann
+claude mcp add --scope user leann-server -- leann_mcp
 # Setup is automatic - just start using Claude Code!
 ```
 Try our fully agentic pipeline with auto query rewriting, semantic search planning, and more:
 
 ![LEANN MCP Integration](assets/mcp_leann.png)
 
-**Ready to supercharge your coding?** [Complete Setup Guide →](packages/leann-mcp/README.md)
+**🔥 Ready to supercharge your coding?** [Complete Setup Guide →](packages/leann-mcp/README.md)
 
 ## 🖥️ Command Line Interface
 
@@ -457,7 +502,8 @@ leann --help
 **To make it globally available:**
 ```bash
 # Install the LEANN CLI globally using uv tool
-uv tool install leann-core
+uv tool install leann-core --with leann
+
 
 # Now you can use leann from anywhere without activating venv
 leann --help
@@ -481,6 +527,9 @@ leann ask my-docs --interactive
 
 # List all your indexes
 leann list
+
+# Remove an index
+leann remove my-docs
 ```
 
 **Key CLI features:**
@@ -493,7 +542,7 @@ leann list
 <details>
 <summary><strong>📋 Click to expand: Complete CLI Reference</strong></summary>
 
-You can use `leann --help`, or `leann build --help`, `leann search --help`, `leann ask --help` to get the complete CLI reference.
+You can use `leann --help`, or `leann build --help`, `leann search --help`, `leann ask --help`, `leann list --help`, `leann remove --help` to get the complete CLI reference.
 
 **Build Command:**
 ```bash
@@ -531,6 +580,31 @@ Options:
   --top-k N                  Retrieval count (default: 20)
 ```
 
+**List Command:**
+```bash
+leann list
+
+# Lists all indexes across all projects with status indicators:
+# ✅ - Index is complete and ready to use
+# ❌ - Index is incomplete or corrupted
+# 📁 - CLI-created index (in .leann/indexes/)
+# 📄 - App-created index (*.leann.meta.json files)
+```
+
+**Remove Command:**
+```bash
+leann remove INDEX_NAME [OPTIONS]
+
+Options:
+  --force, -f    Force removal without confirmation
+
+# Smart removal: automatically finds and safely removes indexes
+# - Shows all matching indexes across projects
+# - Requires confirmation for cross-project removal
+# - Interactive selection when multiple matches found
+# - Supports both CLI and app-created indexes
+```
+
 </details>
 
 ## 🏗️ Architecture & How It Works

apps/base_rag_example.py

@@ -10,6 +10,7 @@ from typing import Any
 
 import dotenv
 from leann.api import LeannBuilder, LeannChat
+from leann.registry import register_project_directory
 from llama_index.core.node_parser import SentenceSplitter
 
 dotenv.load_dotenv()
@@ -214,6 +215,11 @@ class BaseRAGExample(ABC):
         builder.build_index(index_path)
         print(f"Index saved to: {index_path}")
 
+        # Register project directory so leann list can discover this index
+        # The index is saved as args.index_dir/index_name.leann
+        # We want to register the current working directory where the app is run
+        register_project_directory(Path.cwd())
+
         return index_path
 
     async def run_interactive_chat(self, args, index_path: str):

packages/leann-backend-diskann/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-diskann"
-version = "0.2.9"
-dependencies = ["leann-core==0.2.9", "numpy", "protobuf>=3.19.0"]
+version = "0.3.0"
+dependencies = ["leann-core==0.3.0", "numpy", "protobuf>=3.19.0"]
 
 [tool.scikit-build]
 # Key: simplified CMake path

packages/leann-backend-hnsw/pyproject.toml

@@ -6,10 +6,10 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-hnsw"
-version = "0.2.9"
+version = "0.3.0"
 description = "Custom-built HNSW (Faiss) backend for the Leann toolkit."
 dependencies = [
-    "leann-core==0.2.9",
+    "leann-core==0.3.0",
     "numpy",
     "pyzmq>=23.0.0",
     "msgpack>=1.0.0",

packages/leann-core/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann-core"
-version = "0.2.9"
+version = "0.3.0"
 description = "Core API and plugin system for LEANN"
 readme = "README.md"
 requires-python = ">=3.9"

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

@@ -46,6 +46,7 @@ def compute_embeddings(
             - "sentence-transformers": Use sentence-transformers library (default)
             - "mlx": Use MLX backend for Apple Silicon
             - "openai": Use OpenAI embedding API
+            - "gemini": Use Google Gemini embedding API
         use_server: Whether to use embedding server (True for search, False for build)
 
     Returns:
@@ -306,6 +307,23 @@ class LeannBuilder:
     def build_index(self, index_path: str):
         if not self.chunks:
             raise ValueError("No chunks added.")
+
+        # Filter out invalid/empty text chunks early to keep passage and embedding counts aligned
+        valid_chunks: list[dict[str, Any]] = []
+        skipped = 0
+        for chunk in self.chunks:
+            text = chunk.get("text", "")
+            if isinstance(text, str) and text.strip():
+                valid_chunks.append(chunk)
+            else:
+                skipped += 1
+        if skipped > 0:
+            print(
+                f"Warning: Skipping {skipped} empty/invalid text chunk(s). Processing {len(valid_chunks)} valid chunks"
+            )
+            self.chunks = valid_chunks
+            if not self.chunks:
+                raise ValueError("All provided chunks are empty or invalid. Nothing to index.")
         if self.dimensions is None:
             self.dimensions = len(
                 compute_embeddings(
@@ -596,7 +614,7 @@ class LeannSearcher:
             zmq_port=zmq_port,
         )
         # logger.info(f"  Generated embedding shape: {query_embedding.shape}")
-        time.time() - start_time
+        # time.time() - start_time
         # logger.info(f"  Embedding time: {embedding_time} seconds")
 
         start_time = time.time()
@@ -662,8 +680,9 @@ class LeannSearcher:
         This method should be called after you're done using the searcher,
         especially in test environments or batch processing scenarios.
         """
-        if hasattr(self.backend_impl, "embedding_server_manager"):
-            self.backend_impl.embedding_server_manager.stop_server()
+        backend = getattr(self.backend_impl, "embedding_server_manager", None)
+        if backend is not None:
+            backend.stop_server()
 
     # Enable automatic cleanup patterns
     def __enter__(self):

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

@@ -680,6 +680,60 @@ class HFChat(LLMInterface):
         return response.strip()
 
 
+class GeminiChat(LLMInterface):
+    """LLM interface for Google Gemini models."""
+
+    def __init__(self, model: str = "gemini-2.5-flash", api_key: Optional[str] = None):
+        self.model = model
+        self.api_key = api_key or os.getenv("GEMINI_API_KEY")
+
+        if not self.api_key:
+            raise ValueError(
+                "Gemini API key is required. Set GEMINI_API_KEY environment variable or pass api_key parameter."
+            )
+
+        logger.info(f"Initializing Gemini Chat with model='{model}'")
+
+        try:
+            import google.genai as genai
+
+            self.client = genai.Client(api_key=self.api_key)
+        except ImportError:
+            raise ImportError(
+                "The 'google-genai' library is required for Gemini models. Please install it with 'uv pip install google-genai'."
+            )
+
+    def ask(self, prompt: str, **kwargs) -> str:
+        logger.info(f"Sending request to Gemini with model {self.model}")
+
+        try:
+            from google.genai.types import GenerateContentConfig
+
+            generation_config = GenerateContentConfig(
+                temperature=kwargs.get("temperature", 0.7),
+                max_output_tokens=kwargs.get("max_tokens", 1000),
+            )
+
+            # Handle top_p parameter
+            if "top_p" in kwargs:
+                generation_config.top_p = kwargs["top_p"]
+
+            response = self.client.models.generate_content(
+                model=self.model,
+                contents=prompt,
+                config=generation_config,
+            )
+            # Handle potential None response text
+            response_text = response.text
+            if response_text is None:
+                logger.warning("Gemini returned None response text")
+                return ""
+            return response_text.strip()
+        except Exception as e:
+            logger.error(f"Error communicating with Gemini: {e}")
+            return f"Error: Could not get a response from Gemini. Details: {e}"
+
+
 class OpenAIChat(LLMInterface):
     """LLM interface for OpenAI models."""
 
@@ -793,6 +847,8 @@ def get_llm(llm_config: Optional[dict[str, Any]] = None) -> LLMInterface:
         return HFChat(model_name=model or "deepseek-ai/deepseek-llm-7b-chat")
     elif llm_type == "openai":
         return OpenAIChat(model=model or "gpt-4o", api_key=llm_config.get("api_key"))
+    elif llm_type == "gemini":
+        return GeminiChat(model=model or "gemini-2.5-flash", api_key=llm_config.get("api_key"))
     elif llm_type == "simulated":
         return SimulatedChat()
     else:

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

@@ -1,13 +1,14 @@
 import argparse
 import asyncio
 from pathlib import Path
-from typing import Union
+from typing import Optional, Union
 
 from llama_index.core import SimpleDirectoryReader
 from llama_index.core.node_parser import SentenceSplitter
 from tqdm import tqdm
 
 from .api import LeannBuilder, LeannChat, LeannSearcher
+from .registry import register_project_directory
 
 
 def extract_pdf_text_with_pymupdf(file_path: str) -> str:
@@ -84,6 +85,7 @@ Examples:
   leann search my-docs "query"                                           # Search in my-docs index
   leann ask my-docs "question"                                           # Ask my-docs index
   leann list                                                             # List all stored indexes
+  leann remove my-docs                                                   # Remove an index (local first, then global)
             """,
         )
 
@@ -148,6 +150,36 @@ Examples:
             type=str,
             help="Comma-separated list of file extensions to include (e.g., '.txt,.pdf,.pptx'). If not specified, uses default supported types.",
         )
+        build_parser.add_argument(
+            "--include-hidden",
+            action=argparse.BooleanOptionalAction,
+            default=False,
+            help="Include hidden files and directories (paths starting with '.') during indexing (default: false)",
+        )
+        build_parser.add_argument(
+            "--doc-chunk-size",
+            type=int,
+            default=256,
+            help="Document chunk size in tokens/characters (default: 256)",
+        )
+        build_parser.add_argument(
+            "--doc-chunk-overlap",
+            type=int,
+            default=128,
+            help="Document chunk overlap (default: 128)",
+        )
+        build_parser.add_argument(
+            "--code-chunk-size",
+            type=int,
+            default=512,
+            help="Code chunk size in tokens/lines (default: 512)",
+        )
+        build_parser.add_argument(
+            "--code-chunk-overlap",
+            type=int,
+            default=50,
+            help="Code chunk overlap (default: 50)",
+        )
 
         # Search command
         search_parser = subparsers.add_parser("search", help="Search documents")
@@ -221,35 +253,18 @@ Examples:
         # List command
         subparsers.add_parser("list", help="List all indexes")
 
+        # Remove command
+        remove_parser = subparsers.add_parser("remove", help="Remove an index")
+        remove_parser.add_argument("index_name", help="Index name to remove")
+        remove_parser.add_argument(
+            "--force", "-f", action="store_true", help="Force removal without confirmation"
+        )
+
         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)
+        register_project_directory()
 
     def _build_gitignore_parser(self, docs_dir: str):
         """Build gitignore parser using gitignore-parser library."""
@@ -309,8 +324,6 @@ Examples:
             return False
 
     def list_indexes(self):
-        print("Stored LEANN indexes:")
-
         # Get all project directories with .leann
         global_registry = Path.home() / ".leann" / "projects.json"
         all_projects = []
@@ -336,58 +349,326 @@ Examples:
         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> [<dir2> ...]' to create one."
-            )
-            return
-
-        total_indexes = 0
-        current_dir = Path.cwd()
+        # Separate current and other projects
+        other_projects = []
 
         for project_path in valid_projects:
-            indexes_dir = project_path / ".leann" / "indexes"
-            if not indexes_dir.exists():
-                continue
+            if project_path != current_path:
+                other_projects.append(project_path)
 
-            index_dirs = [d for d in indexes_dir.iterdir() if d.is_dir()]
-            if not index_dirs:
-                continue
+        print("📚 LEANN Indexes")
+        print("=" * 50)
 
-            # Show project header
-            if project_path == current_dir:
-                print(f"\n📁 Current project ({project_path}):")
-            else:
-                print(f"\n📂 {project_path}:")
+        total_indexes = 0
+        current_indexes_count = 0
 
-            for index_dir in index_dirs:
+        # Show current project first (most important)
+        print("\n🏠 Current Project")
+        print(f"   {current_path}")
+        print("   " + "─" * 45)
+
+        current_indexes = self._discover_indexes_in_project(current_path)
+        if current_indexes:
+            for idx in current_indexes:
                 total_indexes += 1
-                index_name = index_dir.name
-                meta_file = index_dir / "documents.leann.meta.json"
-                status = "✓" if meta_file.exists() else "✗"
+                current_indexes_count += 1
+                type_icon = "📁" if idx["type"] == "cli" else "📄"
+                print(f"   {current_indexes_count}. {type_icon} {idx['name']} {idx['status']}")
+                if idx["size_mb"] > 0:
+                    print(f"      📦 Size: {idx['size_mb']:.1f} MB")
+        else:
+            print("   📭 No indexes in current project")
 
-                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
+        # Show other projects (reference information)
+        if other_projects:
+            print("\n\n🗂️  Other Projects")
+            print("   " + "─" * 45)
+
+            for project_path in other_projects:
+                project_indexes = self._discover_indexes_in_project(project_path)
+                if not project_indexes:
+                    continue
+
+                print(f"\n   📂 {project_path.name}")
+                print(f"      {project_path}")
+
+                for idx in project_indexes:
+                    total_indexes += 1
+                    type_icon = "📁" if idx["type"] == "cli" else "📄"
+                    print(f"      • {type_icon} {idx['name']} {idx['status']}")
+                    if idx["size_mb"] > 0:
+                        print(f"        📦 {idx['size_mb']:.1f} MB")
+
+        # Summary and usage info
+        print("\n" + "=" * 50)
+        if total_indexes == 0:
+            print("💡 Get started:")
+            print("   leann build my-docs --docs ./documents")
+        else:
+            projects_count = len(
+                [
+                    p
+                    for p in valid_projects
+                    if (p / ".leann" / "indexes").exists()
+                    and list((p / ".leann" / "indexes").iterdir())
+                ]
+            )
+            print(f"📊 Total: {total_indexes} indexes across {projects_count} projects")
+
+            if current_indexes_count > 0:
+                print("\n💫 Quick start (current project):")
+                # Get first index from current project for example
+                current_indexes_dir = current_path / ".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")
+            else:
+                print("\n💡 Create your first index:")
+                print("   leann build my-docs --docs ./documents")
+
+    def _discover_indexes_in_project(self, project_path: Path):
+        """Discover all indexes in a project directory (both CLI and apps formats)"""
+        indexes = []
+
+        # 1. CLI format: .leann/indexes/index_name/
+        cli_indexes_dir = project_path / ".leann" / "indexes"
+        if cli_indexes_dir.exists():
+            for index_dir in cli_indexes_dir.iterdir():
+                if index_dir.is_dir():
+                    meta_file = index_dir / "documents.leann.meta.json"
+                    status = "✅" if meta_file.exists() else "❌"
+
+                    size_mb = 0
+                    if meta_file.exists():
+                        try:
+                            size_mb = sum(
+                                f.stat().st_size for f in index_dir.iterdir() if f.is_file()
+                            ) / (1024 * 1024)
+                        except (OSError, PermissionError):
+                            pass
+
+                    indexes.append(
+                        {
+                            "name": index_dir.name,
+                            "type": "cli",
+                            "status": status,
+                            "size_mb": size_mb,
+                            "path": index_dir,
+                        }
                     )
-                    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):")
+        # 2. Apps format: *.leann.meta.json files anywhere in the project
+        for meta_file in project_path.rglob("*.leann.meta.json"):
+            if meta_file.is_file():
+                # Extract index name from filename (remove .leann.meta.json extension)
+                index_name = meta_file.name.replace(".leann.meta.json", "")
 
-            # 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")
+                # Apps indexes are considered complete if the .leann.meta.json file exists
+                status = "✅"
+
+                # Calculate total size of all related files
+                size_mb = 0
+                try:
+                    index_dir = meta_file.parent
+                    for related_file in index_dir.glob(f"{index_name}.leann*"):
+                        size_mb += related_file.stat().st_size / (1024 * 1024)
+                except (OSError, PermissionError):
+                    pass
+
+                indexes.append(
+                    {
+                        "name": index_name,
+                        "type": "app",
+                        "status": status,
+                        "size_mb": size_mb,
+                        "path": meta_file,
+                    }
+                )
+
+        return indexes
+
+    def remove_index(self, index_name: str, force: bool = False):
+        """Safely remove an index - always show all matches for transparency"""
+
+        # Always do a comprehensive search for safety
+        print(f"🔍 Searching for all indexes named '{index_name}'...")
+        all_matches = self._find_all_matching_indexes(index_name)
+
+        if not all_matches:
+            print(f"❌ Index '{index_name}' not found in any project.")
+            return False
+
+        if len(all_matches) == 1:
+            return self._remove_single_match(all_matches[0], index_name, force)
+        else:
+            return self._remove_from_multiple_matches(all_matches, index_name, force)
+
+    def _find_all_matching_indexes(self, index_name: str):
+        """Find all indexes with the given name across all projects"""
+        matches = []
+
+        # Get all registered projects
+        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
+
+        # Always include current project
+        current_path = Path.cwd()
+        if str(current_path) not in all_projects:
+            all_projects.append(str(current_path))
+
+        # Search across all projects
+        for project_dir in all_projects:
+            project_path = Path(project_dir)
+            if not project_path.exists():
+                continue
+
+            index_dir = project_path / ".leann" / "indexes" / index_name
+            if index_dir.exists():
+                is_current = project_path == current_path
+                matches.append(
+                    {"project_path": project_path, "index_dir": index_dir, "is_current": is_current}
+                )
+
+        # Sort: current project first, then by project name
+        matches.sort(key=lambda x: (not x["is_current"], x["project_path"].name))
+        return matches
+
+    def _remove_single_match(self, match, index_name: str, force: bool):
+        """Handle removal when only one match is found"""
+        project_path = match["project_path"]
+        index_dir = match["index_dir"]
+        is_current = match["is_current"]
+
+        if is_current:
+            location_info = "current project"
+            emoji = "🏠"
+        else:
+            location_info = f"other project '{project_path.name}'"
+            emoji = "📂"
+
+        print(f"✅ Found 1 index named '{index_name}':")
+        print(f"   {emoji} Location: {location_info}")
+        print(f"   📍 Path: {project_path}")
+
+        if not force:
+            if not is_current:
+                print("\n⚠️  CROSS-PROJECT REMOVAL!")
+                print("   This will delete the index from another project.")
+
+            response = input(f"   ❓ Confirm removal from {location_info}? (y/N): ").strip().lower()
+            if response not in ["y", "yes"]:
+                print("   ❌ Removal cancelled.")
+                return False
+
+        return self._delete_index_directory(
+            index_dir, index_name, project_path if not is_current else None
+        )
+
+    def _remove_from_multiple_matches(self, matches, index_name: str, force: bool):
+        """Handle removal when multiple matches are found"""
+
+        print(f"⚠️  Found {len(matches)} indexes named '{index_name}':")
+        print("   " + "─" * 50)
+
+        for i, match in enumerate(matches, 1):
+            project_path = match["project_path"]
+            is_current = match["is_current"]
+
+            if is_current:
+                print(f"   {i}. 🏠 Current project")
+                print(f"      📍 {project_path}")
+            else:
+                print(f"   {i}. 📂 {project_path.name}")
+                print(f"      📍 {project_path}")
+
+            # Show size info
+            try:
+                size_mb = sum(
+                    f.stat().st_size for f in match["index_dir"].iterdir() if f.is_file()
+                ) / (1024 * 1024)
+                print(f"      📦 Size: {size_mb:.1f} MB")
+            except (OSError, PermissionError):
+                pass
+
+        print("   " + "─" * 50)
+
+        if force:
+            print("   ❌ Multiple matches found, but --force specified.")
+            print("   Please run without --force to choose which one to remove.")
+            return False
+
+        try:
+            choice = input(
+                f"   ❓ Which one to remove? (1-{len(matches)}, or 'c' to cancel): "
+            ).strip()
+            if choice.lower() == "c":
+                print("   ❌ Removal cancelled.")
+                return False
+
+            choice_idx = int(choice) - 1
+            if 0 <= choice_idx < len(matches):
+                selected_match = matches[choice_idx]
+                project_path = selected_match["project_path"]
+                index_dir = selected_match["index_dir"]
+                is_current = selected_match["is_current"]
+
+                location = "current project" if is_current else f"'{project_path.name}' project"
+                print(f"   🎯 Selected: Remove from {location}")
+
+                # Final confirmation for safety
+                confirm = input(
+                    f"   ❓ FINAL CONFIRMATION - Type '{index_name}' to proceed: "
+                ).strip()
+                if confirm != index_name:
+                    print("   ❌ Confirmation failed. Removal cancelled.")
+                    return False
+
+                return self._delete_index_directory(
+                    index_dir, index_name, project_path if not is_current else None
+                )
+            else:
+                print("   ❌ Invalid choice. Removal cancelled.")
+                return False
+
+        except (ValueError, KeyboardInterrupt):
+            print("\n   ❌ Invalid input. Removal cancelled.")
+            return False
+
+    def _delete_index_directory(
+        self, index_dir: Path, index_name: str, project_path: Optional[Path] = None
+    ):
+        """Actually delete the index directory"""
+        try:
+            import shutil
+
+            shutil.rmtree(index_dir)
+
+            if project_path:
+                print(f"✅ Index '{index_name}' removed from {project_path.name}")
+            else:
+                print(f"✅ Index '{index_name}' removed successfully")
+            return True
+        except Exception as e:
+            print(f"❌ Error removing index '{index_name}': {e}")
+            return False
 
     def load_documents(
-        self, docs_paths: Union[str, list], custom_file_types: Union[str, None] = None
+        self,
+        docs_paths: Union[str, list],
+        custom_file_types: Union[str, None] = None,
+        include_hidden: bool = False,
     ):
         # Handle both single path (string) and multiple paths (list) for backward compatibility
         if isinstance(docs_paths, str):
@@ -431,6 +712,10 @@ Examples:
 
         all_documents = []
 
+        # Helper to detect hidden path components
+        def _path_has_hidden_segment(p: Path) -> bool:
+            return any(part.startswith(".") and part not in [".", ".."] for part in p.parts)
+
         # First, process individual files if any
         if files:
             print(f"\n🔄 Processing {len(files)} individual file{'s' if len(files) > 1 else ''}...")
@@ -443,8 +728,12 @@ Examples:
 
                 files_by_dir = defaultdict(list)
                 for file_path in files:
-                    parent_dir = str(Path(file_path).parent)
-                    files_by_dir[parent_dir].append(file_path)
+                    file_path_obj = Path(file_path)
+                    if not include_hidden and _path_has_hidden_segment(file_path_obj):
+                        print(f"  ⚠️  Skipping hidden file: {file_path}")
+                        continue
+                    parent_dir = str(file_path_obj.parent)
+                    files_by_dir[parent_dir].append(str(file_path_obj))
 
                 # Load files from each parent directory
                 for parent_dir, file_list in files_by_dir.items():
@@ -455,6 +744,7 @@ Examples:
                         file_docs = SimpleDirectoryReader(
                             parent_dir,
                             input_files=file_list,
+                            # exclude_hidden only affects directory scans; input_files are explicit
                             filename_as_id=True,
                         ).load_data()
                         all_documents.extend(file_docs)
@@ -553,6 +843,8 @@ Examples:
                     # Check if file matches any exclude pattern
                     try:
                         relative_path = file_path.relative_to(docs_path)
+                        if not include_hidden and _path_has_hidden_segment(relative_path):
+                            continue
                         if self._should_exclude_file(relative_path, gitignore_matches):
                             continue
                     except ValueError:
@@ -580,6 +872,7 @@ Examples:
                         try:
                             default_docs = SimpleDirectoryReader(
                                 str(file_path.parent),
+                                exclude_hidden=not include_hidden,
                                 filename_as_id=True,
                                 required_exts=[file_path.suffix],
                             ).load_data()
@@ -608,6 +901,7 @@ Examples:
                     encoding="utf-8",
                     required_exts=code_extensions,
                     file_extractor={},  # Use default extractors
+                    exclude_hidden=not include_hidden,
                     filename_as_id=True,
                 ).load_data(show_progress=True)
 
@@ -726,7 +1020,40 @@ Examples:
             print(f"Index '{index_name}' already exists. Use --force to rebuild.")
             return
 
-        all_texts = self.load_documents(docs_paths, args.file_types)
+        # Configure chunking based on CLI args before loading documents
+        # Guard against invalid configurations
+        doc_chunk_size = max(1, int(args.doc_chunk_size))
+        doc_chunk_overlap = max(0, int(args.doc_chunk_overlap))
+        if doc_chunk_overlap >= doc_chunk_size:
+            print(
+                f"⚠️  Adjusting doc chunk overlap from {doc_chunk_overlap} to {doc_chunk_size - 1} (must be < chunk size)"
+            )
+            doc_chunk_overlap = doc_chunk_size - 1
+
+        code_chunk_size = max(1, int(args.code_chunk_size))
+        code_chunk_overlap = max(0, int(args.code_chunk_overlap))
+        if code_chunk_overlap >= code_chunk_size:
+            print(
+                f"⚠️  Adjusting code chunk overlap from {code_chunk_overlap} to {code_chunk_size - 1} (must be < chunk size)"
+            )
+            code_chunk_overlap = code_chunk_size - 1
+
+        self.node_parser = SentenceSplitter(
+            chunk_size=doc_chunk_size,
+            chunk_overlap=doc_chunk_overlap,
+            separator=" ",
+            paragraph_separator="\n\n",
+        )
+        self.code_parser = SentenceSplitter(
+            chunk_size=code_chunk_size,
+            chunk_overlap=code_chunk_overlap,
+            separator="\n",
+            paragraph_separator="\n\n",
+        )
+
+        all_texts = self.load_documents(
+            docs_paths, args.file_types, include_hidden=args.include_hidden
+        )
         if not all_texts:
             print("No documents found")
             return
@@ -863,6 +1190,8 @@ Examples:
 
         if args.command == "list":
             self.list_indexes()
+        elif args.command == "remove":
+            self.remove_index(args.index_name, args.force)
         elif args.command == "build":
             await self.build_index(args)
         elif args.command == "search":
@@ -874,10 +1203,15 @@ Examples:
 
 
 def main():
+    import logging
+
     import dotenv
 
     dotenv.load_dotenv()
 
+    # Set clean logging for CLI usage
+    logging.getLogger().setLevel(logging.WARNING)  # Only show warnings and errors
+
     cli = LeannCLI()
     asyncio.run(cli.run())
 

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

@@ -57,6 +57,8 @@ def compute_embeddings(
         return compute_embeddings_mlx(texts, model_name)
     elif mode == "ollama":
         return compute_embeddings_ollama(texts, model_name, is_build=is_build)
+    elif mode == "gemini":
+        return compute_embeddings_gemini(texts, model_name, is_build=is_build)
     else:
         raise ValueError(f"Unsupported embedding mode: {mode}")
 
@@ -244,6 +246,16 @@ def compute_embeddings_openai(texts: list[str], model_name: str) -> np.ndarray:
     except ImportError as e:
         raise ImportError(f"OpenAI package not installed: {e}")
 
+    # Validate input list
+    if not texts:
+        raise ValueError("Cannot compute embeddings for empty text list")
+    # Extra validation: abort early if any item is empty/whitespace
+    invalid_count = sum(1 for t in texts if not isinstance(t, str) or not t.strip())
+    if invalid_count > 0:
+        raise ValueError(
+            f"Found {invalid_count} empty/invalid text(s) in input. Upstream should filter before calling OpenAI."
+        )
+
     api_key = os.getenv("OPENAI_API_KEY")
     if not api_key:
         raise RuntimeError("OPENAI_API_KEY environment variable not set")
@@ -263,8 +275,16 @@ def compute_embeddings_openai(texts: list[str], model_name: str) -> np.ndarray:
     print(f"len of texts: {len(texts)}")
 
     # OpenAI has limits on batch size and input length
-    max_batch_size = 1000  # Conservative batch size
+    max_batch_size = 800  # Conservative batch size because the token limit is 300K
     all_embeddings = []
+    # get the avg len of texts
+    avg_len = sum(len(text) for text in texts) / len(texts)
+    print(f"avg len of texts: {avg_len}")
+    # if avg len is less than 1000, use the max batch size
+    if avg_len > 300:
+        max_batch_size = 500
+
+    # if avg len is less than 1000, use the max batch size
 
     try:
         from tqdm import tqdm
@@ -650,3 +670,83 @@ def compute_embeddings_ollama(
     logger.info(f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}")
 
     return embeddings
+
+
+def compute_embeddings_gemini(
+    texts: list[str], model_name: str = "text-embedding-004", is_build: bool = False
+) -> np.ndarray:
+    """
+    Compute embeddings using Google Gemini API.
+
+    Args:
+        texts: List of texts to compute embeddings for
+        model_name: Gemini model name (default: "text-embedding-004")
+        is_build: Whether this is a build operation (shows progress bar)
+
+    Returns:
+        Embeddings array, shape: (len(texts), embedding_dim)
+    """
+    try:
+        import os
+
+        import google.genai as genai
+    except ImportError as e:
+        raise ImportError(f"Google GenAI package not installed: {e}")
+
+    api_key = os.getenv("GEMINI_API_KEY")
+    if not api_key:
+        raise RuntimeError("GEMINI_API_KEY environment variable not set")
+
+    # Cache Gemini client
+    cache_key = "gemini_client"
+    if cache_key in _model_cache:
+        client = _model_cache[cache_key]
+    else:
+        client = genai.Client(api_key=api_key)
+        _model_cache[cache_key] = client
+        logger.info("Gemini client cached")
+
+    logger.info(
+        f"Computing embeddings for {len(texts)} texts using Gemini API, model: '{model_name}'"
+    )
+
+    # Gemini supports batch embedding
+    max_batch_size = 100  # Conservative batch size for Gemini
+    all_embeddings = []
+
+    try:
+        from tqdm import tqdm
+
+        total_batches = (len(texts) + max_batch_size - 1) // max_batch_size
+        batch_range = range(0, len(texts), max_batch_size)
+        batch_iterator = tqdm(
+            batch_range, desc="Computing embeddings", unit="batch", total=total_batches
+        )
+    except ImportError:
+        # Fallback when tqdm is not available
+        batch_iterator = range(0, len(texts), max_batch_size)
+
+    for i in batch_iterator:
+        batch_texts = texts[i : i + max_batch_size]
+
+        try:
+            # Use the embed_content method from the new Google GenAI SDK
+            response = client.models.embed_content(
+                model=model_name,
+                contents=batch_texts,
+                config=genai.types.EmbedContentConfig(
+                    task_type="RETRIEVAL_DOCUMENT"  # For document embedding
+                ),
+            )
+
+            # Extract embeddings from response
+            for embedding_data in response.embeddings:
+                all_embeddings.append(embedding_data.values)
+        except Exception as e:
+            logger.error(f"Batch {i} failed: {e}")
+            raise
+
+    embeddings = np.array(all_embeddings, dtype=np.float32)
+    logger.info(f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}")
+
+    return embeddings

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

@@ -64,19 +64,6 @@ def handle_request(request):
                             "required": ["index_name", "query"],
                         },
                     },
-                    {
-                        "name": "leann_status",
-                        "description": "📊 Check the health and stats of your code indexes - like a medical checkup for your codebase knowledge!",
-                        "inputSchema": {
-                            "type": "object",
-                            "properties": {
-                                "index_name": {
-                                    "type": "string",
-                                    "description": "Optional: Name of specific index to check. If not provided, shows status of all indexes.",
-                                }
-                            },
-                        },
-                    },
                     {
                         "name": "leann_list",
                         "description": "📋 Show all your indexed codebases - your personal code library! Use this to see what's available for search.",
@@ -118,15 +105,6 @@ def handle_request(request):
                 ]
                 result = subprocess.run(cmd, capture_output=True, text=True)
 
-            elif tool_name == "leann_status":
-                if args.get("index_name"):
-                    # Check specific index status - for now, we'll use leann list and filter
-                    result = subprocess.run(["leann", "list"], capture_output=True, text=True)
-                    # We could enhance this to show more detailed status per index
-                else:
-                    # Show all indexes status
-                    result = subprocess.run(["leann", "list"], capture_output=True, text=True)
-
             elif tool_name == "leann_list":
                 result = subprocess.run(["leann", "list"], capture_output=True, text=True)
 

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

@@ -2,11 +2,17 @@
 
 import importlib
 import importlib.metadata
-from typing import TYPE_CHECKING
+import json
+import logging
+from pathlib import Path
+from typing import TYPE_CHECKING, Optional, Union
 
 if TYPE_CHECKING:
     from leann.interface import LeannBackendFactoryInterface
 
+# Set up logger for this module
+logger = logging.getLogger(__name__)
+
 BACKEND_REGISTRY: dict[str, "LeannBackendFactoryInterface"] = {}
 
 
@@ -14,7 +20,7 @@ def register_backend(name: str):
     """A decorator to register a new backend class."""
 
     def decorator(cls):
-        print(f"INFO: Registering backend '{name}'")
+        logger.debug(f"Registering backend '{name}'")
         BACKEND_REGISTRY[name] = cls
         return cls
 
@@ -39,3 +45,54 @@ def autodiscover_backends():
             # print(f"WARN: Could not import backend module '{backend_module_name}': {e}")
             pass
     # print("INFO: Backend auto-discovery finished.")
+
+
+def register_project_directory(project_dir: Optional[Union[str, Path]] = None):
+    """
+    Register a project directory in the global LEANN registry.
+
+    This allows `leann list` to discover indexes created by apps or other tools.
+
+    Args:
+        project_dir: Directory to register. If None, uses current working directory.
+    """
+    if project_dir is None:
+        project_dir = Path.cwd()
+    else:
+        project_dir = Path(project_dir)
+
+    # Only register directories that have some kind of LEANN content
+    # Either .leann/indexes/ (CLI format) or *.leann.meta.json files (apps format)
+    has_cli_indexes = (project_dir / ".leann" / "indexes").exists()
+    has_app_indexes = any(project_dir.rglob("*.leann.meta.json"))
+
+    if not (has_cli_indexes or has_app_indexes):
+        # Don't register if there are no LEANN indexes
+        return
+
+    global_registry = Path.home() / ".leann" / "projects.json"
+    global_registry.parent.mkdir(exist_ok=True)
+
+    project_str = str(project_dir.resolve())
+
+    # Load existing registry
+    projects = []
+    if global_registry.exists():
+        try:
+            with open(global_registry) as f:
+                projects = json.load(f)
+        except Exception:
+            logger.debug("Could not load existing project registry")
+            projects = []
+
+    # Add project if not already present
+    if project_str not in projects:
+        projects.append(project_str)
+
+        # Save updated registry
+        try:
+            with open(global_registry, "w") as f:
+                json.dump(projects, f, indent=2)
+            logger.debug(f"Registered project directory: {project_str}")
+        except Exception as e:
+            logger.warning(f"Could not save project registry: {e}")

packages/leann-mcp/README.md

@@ -13,10 +13,20 @@ This installs the `leann` CLI into an isolated tool environment and includes bot
 
 ## 🚀 Quick Setup
 
-Add the LEANN MCP server to Claude Code:
+Add the LEANN MCP server to Claude Code. Choose the scope based on how widely you want it available. Below is the command to install it globally; if you prefer a local install, skip this step:
 
 ```bash
-claude mcp add leann-server -- leann_mcp
+# Global (recommended): available in all projects for your user
+claude mcp add --scope user leann-server -- leann_mcp
+```
+
+- `leann-server`: the display name of the MCP server in Claude Code (you can change it).
+- `leann_mcp`: the Python entry point installed with LEANN that starts the MCP server.
+
+Verify it is registered globally:
+
+```bash
+claude mcp list | cat
 ```
 
 ## 🛠️ Available Tools
@@ -25,27 +35,36 @@ Once connected, you'll have access to these powerful semantic search tools in Cl
 
 - **`leann_list`** - List all available indexes across your projects
 - **`leann_search`** - Perform semantic searches across code and documents
-- **`leann_ask`** - Ask natural language questions and get AI-powered answers from your codebase
+
 
 ## 🎯 Quick Start Example
 
 ```bash
+# Add locally if you did not add it globally (current folder only; default if --scope is omitted)
+claude mcp add leann-server -- leann_mcp
+
 # Build an index for your project (change to your actual path)
-leann build my-project --docs ./
+# See the advanced examples below for more ways to configure indexing
+# Set the index name (replace 'my-project' with your own)
+leann build my-project --docs $(git ls-files)
 
 # Start Claude Code
 claude
 ```
 
-## 🚀 Advanced Usage Examples
+## 🚀 Advanced Usage Examples to build the index
 
 ### Index Entire Git Repository
 ```bash
-# Index all tracked files in your git repository, note right now we will skip submodules, but we can add it back easily if you want
+# Index all tracked files in your Git repository.
+# Note: submodules are currently skipped; we can add them back if needed.
 leann build my-repo --docs $(git ls-files) --embedding-mode sentence-transformers --embedding-model all-MiniLM-L6-v2 --backend hnsw
 
-# Index only specific file types from git
+# Index only tracked Python files from Git.
 leann build my-python-code --docs $(git ls-files "*.py") --embedding-mode sentence-transformers --embedding-model all-MiniLM-L6-v2 --backend hnsw
+
+# If you encounter empty requests caused by empty files (e.g., __init__.py), exclude zero-byte files. Thanks @ww2283 for pointing [that](https://github.com/yichuan-w/LEANN/issues/48) out
+leann build leann-prospec-lig --docs $(find ./src -name "*.py" -not -empty) --embedding-mode openai --embedding-model text-embedding-3-small
 ```
 
 ### Multiple Directories and Files
@@ -73,7 +92,7 @@ leann build docs-and-configs --docs $(git ls-files "*.md" "*.yml" "*.yaml" "*.js
 ```
 
 
-**Try this in Claude Code:**
+## **Try this in Claude Code:**
 ```
 Help me understand this codebase. List available indexes and search for authentication patterns.
 ```
@@ -82,6 +101,7 @@ Help me understand this codebase. List available indexes and search for authenti
   <img src="../../assets/claude_code_leann.png" alt="LEANN in Claude Code" width="80%">
 </p>
 
+If you see a prompt asking whether to proceed with LEANN, you can now use it in your chat!
 
 ## 🧠 How It Works
 
@@ -117,3 +137,11 @@ To remove LEANN
 ```
 uv pip uninstall leann leann-backend-hnsw leann-core
 ```
+
+To globally remove LEANN (for version update)
+```
+uv tool list | cat
+uv tool uninstall leann-core
+command -v leann || echo "leann gone"
+command -v leann_mcp || echo "leann_mcp gone"
+```

packages/leann/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann"
-version = "0.2.9"
+version = "0.3.0"
 description = "LEANN - The smallest vector index in the world. RAG Everything with LEANN!"
 readme = "README.md"
 requires-python = ">=3.9"

packages/wechat-exporter/__init__.py

@@ -0,0 +1 @@
+__all__ = []

packages/wechat-exporter/main.py

@@ -136,5 +136,9 @@ def export_sqlite(
     connection.commit()
 
 
-if __name__ == "__main__":
+def main():
     app()
+
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -10,11 +10,10 @@ requires-python = ">=3.9"
 dependencies = [
     "leann-core",
     "leann-backend-hnsw",
+    "typer>=0.12.3",
     "numpy>=1.26.0",
     "torch",
     "tqdm",
-    "flask",
-    "flask_compress",
     "datasets>=2.15.0",
     "evaluate",
     "colorama",
@@ -65,9 +64,7 @@ test = [
     "pytest>=7.0",
     "pytest-timeout>=2.0",
     "llama-index-core>=0.12.0",
-    "llama-index-readers-file>=0.4.0",
     "python-dotenv>=1.0.0",
-    "sentence-transformers>=2.2.0",
 ]
 
 diskann = [
@@ -84,6 +81,11 @@ documents = [
 
 [tool.setuptools]
 py-modules = []
+packages = ["wechat_exporter"]
+package-dir = { "wechat_exporter" = "packages/wechat-exporter" }
+
+[project.scripts]
+wechat-exporter = "wechat_exporter.main:main"
 
 
 [tool.uv.sources]
@@ -94,13 +96,8 @@ leann-backend-hnsw = { path = "packages/leann-backend-hnsw", editable = true }
 [tool.ruff]
 target-version = "py39"
 line-length = 100
-extend-exclude = [
-    "third_party",
-    "*.egg-info",
-    "__pycache__",
-    ".git",
-    ".venv",
-]
+extend-exclude = ["third_party"]
+
 
 [tool.ruff.lint]
 select = [
@@ -123,21 +120,12 @@ ignore = [
     "RUF012", # mutable class attributes should be annotated with typing.ClassVar
 ]
 
-[tool.ruff.lint.per-file-ignores]
-"test/**/*.py" = ["E402"]      # module level import not at top of file (common in tests)
-"examples/**/*.py" = ["E402"]  # module level import not at top of file (common in examples)
-
 [tool.ruff.format]
 quote-style = "double"
 indent-style = "space"
 skip-magic-trailing-comma = false
 line-ending = "auto"
 
-[dependency-groups]
-dev = [
-    "ruff>=0.12.4",
-]
-
 [tool.lychee]
 accept = ["200", "403", "429", "503"]
 timeout = 20