🔗 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>

pyproject.toml

@@ -14,8 +14,6 @@ dependencies = [
     "numpy>=1.26.0",
     "torch",
     "tqdm",
-    "flask",
-    "flask_compress",
     "datasets>=2.15.0",
     "evaluate",
     "colorama",
@@ -66,9 +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 = [
@@ -100,13 +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 = [
@@ -129,21 +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