feat: Add pycli bash wrapper with hierarchical vector database support

- Create unified bash wrapper (pycli) for Python CLI tools
- Implement hierarchical vector database with smart parent discovery
- Add comprehensive installation script with auto-configuration
- Remove redundant analyzer.py and api_indexer.py files
- Enhance Python scripts with environment variable support
- Update documentation to focus on pycli unified interface

Key Features:
- Automatic parent directory vector DB discovery
- No redundant vectorization in subdirectories
- Central vector database storage in ~/.claude/vector_db
- Configurable Python interpreter paths
- One-command installation and setup

🤖 Generated with Claude Code

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

.claude/scripts/README.md

@@ -0,0 +1,152 @@
+# pycli - Python CLI Wrapper with Hierarchical Vector Database
+
+This directory contains the bash wrapper and configuration for the enhanced Python-based analysis CLI with hierarchical vector database support.
+
+## 📁 Files
+
+- **`pycli`** - Main bash wrapper script
+- **`pycli.conf`** - Configuration file
+- **`install_pycli.sh`** - Installation script
+- **`README.md`** - This documentation
+
+## 🚀 Quick Installation
+
+```bash
+# Run the installation script
+bash install_pycli.sh
+
+# Follow the prompts to configure your shell
+# The script will automatically detect your Python installation
+
+# Verify installation
+pycli --help
+```
+
+## 🎯 Key Features
+
+### Hierarchical Vector Database
+- **Smart Parent Discovery**: Subdirectories automatically use parent's vector database
+- **No Redundant Processing**: Avoids duplicate vectorization in project subdirectories
+- **Central Storage**: All vector databases stored in `~/.claude/vector_db/`
+- **Path-based Organization**: Organized by project directory structure
+
+### Unified Interface
+- **Single Command**: `pycli` replaces complex Python script calls
+- **Intelligent Context**: Automatic file discovery with semantic search
+- **Tool Integration**: Seamless integration with Gemini and Codex
+- **Configuration Management**: Environment-specific Python interpreter paths
+
+## 📋 Common Commands
+
+```bash
+# Initialize new project
+cd /path/to/your/project
+pycli --init
+
+# Smart analysis
+pycli --analyze --query "authentication patterns" --tool gemini
+
+# Direct analysis
+pycli --analyze --tool codex -p "implement user login"
+
+# Maintenance
+pycli --update-embeddings
+pycli --status
+```
+
+## 🔧 Configuration
+
+Edit `~/.claude/scripts/pycli.conf` after installation:
+
+```bash
+# Python interpreter path
+PYTHON_PATH="/usr/bin/python3"
+
+# Vector database root directory
+VECTOR_DB_ROOT="$HOME/.claude/vector_db"
+
+# Python scripts directory
+PYTHON_SCRIPT_DIR="$HOME/.claude/python_script"
+```
+
+## 🏗️ How Hierarchical DB Works
+
+```
+Project Structure:          Vector Database:
+/home/user/myproject/       ~/.claude/vector_db/
+├── src/                    └── home_user_myproject/
+│   ├── auth/                   ├── embeddings.pkl
+│   └── api/                    └── index.json
+└── tests/
+
+# All subdirectories use the single parent DB
+```
+
+## 📖 Documentation
+
+For complete usage information, see:
+- **Strategy Guide**: `~/.claude/workflows/python-tools-strategy.md`
+- **Installation Guide**: Run `bash install_pycli.sh` for guided setup
+
+## 🎪 Migration from Legacy Tools
+
+```bash
+# Replace gemini-wrapper
+# OLD: ~/.claude/scripts/gemini-wrapper -p "prompt"
+# NEW: pycli --analyze --tool gemini -p "prompt"
+
+# Replace codex commands
+# OLD: codex --full-auto exec "task"
+# NEW: pycli --analyze --tool codex -p "task"
+
+# Enhanced with context discovery
+pycli --analyze --query "relevant context" --tool both
+```
+
+## 🐛 Troubleshooting
+
+```bash
+# Check system status
+pycli --status
+
+# Rebuild everything
+pycli --init
+
+# Test search functionality
+pycli --test-search
+
+# View configuration
+cat ~/.claude/scripts/pycli.conf
+```
+
+## 💡 Advanced Usage
+
+### Project Integration
+```bash
+# Add to package.json
+{
+  "scripts": {
+    "analyze": "pycli --analyze --query",
+    "ai-init": "pycli --init",
+    "ai-update": "pycli --update-embeddings"
+  }
+}
+
+# Use in Makefiles
+analyze:
+	pycli --analyze --query "$(QUERY)" --tool gemini
+```
+
+### CI/CD Integration
+```yaml
+# GitHub Actions example
+- name: Update AI Context
+  run: pycli --update-embeddings
+
+- name: Analyze Changes
+  run: pycli --analyze --query "code review" --tool gemini
+```
+
+---
+
+For questions or issues, check the documentation or run `pycli --help`.