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/pycli.conf

@@ -0,0 +1,159 @@
+#==============================================================================
+# pycli Configuration File
+#
+# This file contains configuration settings for the pycli bash wrapper.
+# Modify these settings according to your environment.
+#==============================================================================
+
+#------------------------------------------------------------------------------
+# Python Environment Configuration
+#------------------------------------------------------------------------------
+
+# Path to Python interpreter
+# Examples:
+#   - System Python: /usr/bin/python3
+#   - Conda: /opt/conda/bin/python
+#   - Virtual env: /home/user/.virtualenvs/myenv/bin/python
+#   - Windows: /c/Python39/python.exe
+PYTHON_PATH="/usr/bin/python3"
+
+# Alternative Python paths for different environments
+# Uncomment and modify as needed:
+# PYTHON_PATH="/opt/conda/bin/python"              # Conda
+# PYTHON_PATH="$HOME/.pyenv/versions/3.11.0/bin/python"  # pyenv
+# PYTHON_PATH="/c/Python311/python.exe"           # Windows
+
+#------------------------------------------------------------------------------
+# Directory Configuration
+#------------------------------------------------------------------------------
+
+# Python script location (should point to ~/.claude/python_script)
+PYTHON_SCRIPT_DIR="$HOME/.claude/python_script"
+
+# Central vector database storage location
+VECTOR_DB_ROOT="$HOME/.claude/vector_db"
+
+# Cache directory for temporary files
+CACHE_DIR="$HOME/.claude/cache"
+
+#------------------------------------------------------------------------------
+# Default Tool Settings
+#------------------------------------------------------------------------------
+
+# Default tool to use when not specified
+# Options: gemini, codex, both
+DEFAULT_TOOL="gemini"
+
+# Default number of similar files to return in vector search
+DEFAULT_TOP_K="10"
+
+# Default similarity threshold for vector search (0.0-1.0)
+SIMILARITY_THRESHOLD="0.3"
+
+# Default timeout for tool execution (seconds)
+TOOL_TIMEOUT="300"
+
+#------------------------------------------------------------------------------
+# Vector Database Configuration
+#------------------------------------------------------------------------------
+
+# Enable hierarchical vector database mode
+# When true, subdirectories will use parent directory's vector database
+HIERARCHICAL_MODE="true"
+
+# Maximum depth to search for parent vector databases
+MAX_SEARCH_DEPTH="10"
+
+# Minimum files required to create a separate vector database
+MIN_FILES_FOR_SEPARATE_DB="50"
+
+#------------------------------------------------------------------------------
+# Performance Settings
+#------------------------------------------------------------------------------
+
+# Enable verbose output for debugging
+# Set to "1" to enable, "0" to disable
+PYCLI_VERBOSE="0"
+
+# Enable caching of analysis results
+ENABLE_CACHING="true"
+
+# Cache TTL in seconds (1 hour default)
+CACHE_TTL="3600"
+
+#------------------------------------------------------------------------------
+# Integration Settings
+#------------------------------------------------------------------------------
+
+# Gemini wrapper compatibility mode
+# Set to "true" to enable compatibility with existing gemini-wrapper scripts
+GEMINI_COMPAT_MODE="true"
+
+# Codex integration settings
+CODEX_COMPAT_MODE="true"
+
+# Auto-build index if not found
+AUTO_BUILD_INDEX="true"
+
+# Auto-update embeddings when files change
+AUTO_UPDATE_EMBEDDINGS="true"
+
+#------------------------------------------------------------------------------
+# Logging Configuration
+#------------------------------------------------------------------------------
+
+# Log level: DEBUG, INFO, WARNING, ERROR
+LOG_LEVEL="INFO"
+
+# Log file location
+LOG_FILE="$HOME/.claude/logs/pycli.log"
+
+# Enable log rotation
+ENABLE_LOG_ROTATION="true"
+
+# Maximum log file size (MB)
+MAX_LOG_SIZE="10"
+
+#------------------------------------------------------------------------------
+# Advanced Configuration
+#------------------------------------------------------------------------------
+
+# Custom configuration file for Python scripts
+# Leave empty to use default config.yaml
+PYTHON_CONFIG_FILE=""
+
+# Additional Python path directories
+# Uncomment and modify if you need to add custom modules
+# ADDITIONAL_PYTHON_PATH="/path/to/custom/modules"
+
+# Environment variables to pass to Python scripts
+# Uncomment and modify as needed
+# CUSTOM_ENV_VAR1="value1"
+# CUSTOM_ENV_VAR2="value2"
+
+#------------------------------------------------------------------------------
+# Platform-Specific Settings
+#------------------------------------------------------------------------------
+
+# Windows-specific settings
+if [[ "$OSTYPE" == "msys" ]] || [[ "$OSTYPE" == "cygwin" ]]; then
+    # Adjust paths for Windows
+    VECTOR_DB_ROOT="${VECTOR_DB_ROOT//\\//}"
+    PYTHON_SCRIPT_DIR="${PYTHON_SCRIPT_DIR//\\//}"
+fi
+
+# macOS-specific settings
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    # macOS-specific optimizations
+    export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES
+fi
+
+#------------------------------------------------------------------------------
+# User Customization
+#------------------------------------------------------------------------------
+
+# Load user-specific configuration if it exists
+USER_CONFIG="$HOME/.claude/config/pycli.user.conf"
+if [[ -f "$USER_CONFIG" ]]; then
+    source "$USER_CONFIG"
+fi