🔗 Auto-register apps: Universal index discovery (#64)

* feat: Enhance CLI with improved list and smart remove commands

## ✨ New Features

### 🏠 Enhanced `leann list` command
- **Better UX**: Current project shown first with clear separation
- **Visual improvements**: Icons (🏠/📂), better formatting, size info
- **Smart guidance**: Context-aware usage examples and getting started tips

### 🛡️ Smart `leann remove` command
- **Safety first**: Always shows ALL matching indexes across projects
- **Intelligent handling**:
  - Single match: Clear location display with cross-project warnings
  - Multiple matches: Interactive selection with final confirmation
- **Prevents accidents**: No more deleting wrong indexes due to name conflicts
- **User-friendly**: 'c' to cancel, clear visual hierarchy, detailed info

### 🔧 Technical improvements
- **Clean logging**: Hide debug messages for better CLI experience
- **Comprehensive search**: Always scan all projects for transparency
- **Error handling**: Graceful handling of edge cases and user input

## 🎯 Impact
- **Safer**: Eliminates risk of accidental index deletion
- **Clearer**: Users always know what they're operating on
- **Smarter**: Automatic detection and handling of common scenarios

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

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

* chore: vscode ruff, and format

---------

Co-authored-by: Claude <noreply@anthropic.com>

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

@@ -2,8 +2,10 @@
 
 import importlib
 import importlib.metadata
+import json
 import logging
-from typing import TYPE_CHECKING
+from pathlib import Path
+from typing import TYPE_CHECKING, Optional, Union
 
 if TYPE_CHECKING:
     from leann.interface import LeannBackendFactoryInterface
@@ -43,3 +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}")