feat: Add comprehensive dynamic configuration system v3.3.0

## Major Features Added

### 🎯 Dynamic Configuration System
- **Environment-aware model selection**: DEFAULT_MODEL with 'pro'/'flash' shortcuts
- **Configurable thinking modes**: DEFAULT_THINKING_MODE_THINKDEEP for extended reasoning
- **All tool schemas now dynamic**: Show actual current defaults instead of hardcoded values
- **Enhanced setup workflow**: Copy from .env.example with smart customization

### 🔧 Model & Thinking Configuration
- **Smart model resolution**: Support both shortcuts ('pro', 'flash') and full model names
- **Thinking mode optimization**: Only apply thinking budget to models that support it
- **Flash model compatibility**: Works without thinking config, still beneficial via system prompts
- **Dynamic schema descriptions**: Tool parameters show current environment values

### 🚀 Enhanced Developer Experience
- **Fail-fast Docker setup**: GEMINI_API_KEY required upfront in docker-compose
- **Comprehensive startup logging**: Shows current model and thinking mode defaults
- **Enhanced get_version tool**: Reports all dynamic configuration values
- **Better .env documentation**: Clear token consumption details and model options

### 🧪 Comprehensive Testing
- **Live model validation**: New simulator test validates Pro vs Flash thinking behavior
- **Dynamic configuration tests**: Verify environment variable overrides work correctly
- **Complete test coverage**: All 139 unit tests pass, including new model config tests

### 📋 Configuration Files Updated
- **docker-compose.yml**: Fail-fast API key validation, thinking mode support
- **setup-docker.sh**: Copy from .env.example instead of manual creation
- **.env.example**: Detailed documentation with token consumption per thinking mode
- **.gitignore**: Added test-setup/ for cleanup

### 🛠 Technical Improvements
- **Removed setup.py**: Fully Docker-based deployment (no longer needed)
- **REDIS_URL smart defaults**: Auto-configured for Docker, still configurable for dev
- **All tools updated**: Consistent dynamic model parameter descriptions
- **Enhanced error handling**: Better model resolution and validation

## Breaking Changes
- Removed setup.py (Docker-only deployment)
- Model parameter descriptions now show actual defaults (dynamic)

## Migration Guide
- Update .env files using new .env.example format
- Use 'pro'/'flash' shortcuts or full model names
- Set DEFAULT_THINKING_MODE_THINKDEEP for custom thinking depth

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

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

setup-docker.sh

@@ -17,41 +17,34 @@ if [ -f .env ]; then
     echo "⚠️  .env file already exists! Updating if needed..."
     echo ""
 else
-    # Check if GEMINI_API_KEY is already set in environment
-    if [ -n "$GEMINI_API_KEY" ]; then
-        API_KEY_VALUE="$GEMINI_API_KEY"
-        echo "✅ Found existing GEMINI_API_KEY in environment"
-    else
-        API_KEY_VALUE="your-gemini-api-key-here"
+    # Copy from .env.example and customize
+    if [ ! -f .env.example ]; then
+        echo "❌ .env.example file not found! This file should exist in the project directory."
+        exit 1
     fi
     
-    # Create the .env file
-    cat > .env << EOF
-# Gemini MCP Server Docker Environment Configuration
-# Generated on $(date)
-
-# Your Gemini API key (get one from https://makersuite.google.com/app/apikey)
-# IMPORTANT: Replace this with your actual API key
-GEMINI_API_KEY=$API_KEY_VALUE
-
-# Redis configuration (automatically set for Docker Compose)
-REDIS_URL=redis://redis:6379/0
-
-# Workspace root - host path that maps to /workspace in container
-# This should be the host directory path that contains all files Claude might reference
-# We use $HOME (not $PWD) because Claude needs access to ANY absolute file path,
-# not just files within the current project directory. Additionally, Claude Code
-# could be running from multiple locations at the same time.
-WORKSPACE_ROOT=$HOME
-
-# Logging level (DEBUG, INFO, WARNING, ERROR)
-# DEBUG: Shows detailed operational messages, conversation threading, tool execution flow
-# INFO: Shows general operational messages (default)
-# WARNING: Shows only warnings and errors
-# ERROR: Shows only errors
-# Uncomment and change to DEBUG if you need detailed troubleshooting information
-LOG_LEVEL=INFO
-EOF
+    # Copy .env.example to .env
+    cp .env.example .env
+    echo "✅ Created .env from .env.example"
+    
+    # Customize the API key if it's set in environment
+    if [ -n "$GEMINI_API_KEY" ]; then
+        # Replace the placeholder API key with the actual value
+        if command -v sed >/dev/null 2>&1; then
+            sed -i.bak "s/your_gemini_api_key_here/$GEMINI_API_KEY/" .env && rm .env.bak
+            echo "✅ Updated .env with existing GEMINI_API_KEY from environment"
+        else
+            echo "⚠️  Found GEMINI_API_KEY in environment, but sed not available. Please update .env manually."
+        fi
+    else
+        echo "⚠️  GEMINI_API_KEY not found in environment. Please edit .env and add your API key."
+    fi
+    
+    # Update WORKSPACE_ROOT to use current user's home directory
+    if command -v sed >/dev/null 2>&1; then
+        sed -i.bak "s|WORKSPACE_ROOT=/Users/your-username|WORKSPACE_ROOT=$HOME|" .env && rm .env.bak
+        echo "✅ Updated WORKSPACE_ROOT to $HOME"
+    fi
     echo "✅ Created .env file with Redis configuration"
     echo ""
 fi