Easier access to logs at startup with -f on the run script

Improved prompt for immediate action
Additional logging of tool names
Updated documentation
Context aware decomposition system prompt
New script to run code quality checks

code_quality_checks.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# Zen MCP Server - Code Quality Checks
+# This script runs all required linting and testing checks before committing changes.
+# ALL checks must pass 100% for CI/CD to succeed.
+
+set -e  # Exit on any error
+
+echo "🔍 Running Code Quality Checks for Zen MCP Server"
+echo "================================================="
+
+# Check if virtual environment is activated
+if [[ "$VIRTUAL_ENV" == "" ]]; then
+    echo "❌ Virtual environment not activated!"
+    echo "Please run: source venv/bin/activate"
+    exit 1
+fi
+
+echo "✅ Virtual environment detected: $VIRTUAL_ENV"
+echo ""
+
+# Step 1: Linting and Formatting
+echo "📋 Step 1: Running Linting and Formatting Checks"
+echo "--------------------------------------------------"
+
+echo "🔧 Running ruff linting with auto-fix..."
+ruff check --fix
+
+echo "🎨 Running black code formatting..."
+black .
+
+echo "📦 Running import sorting with isort..."
+isort .
+
+echo "✅ Verifying all linting passes..."
+ruff check
+
+echo "✅ Step 1 Complete: All linting and formatting checks passed!"
+echo ""
+
+# Step 2: Unit Tests
+echo "🧪 Step 2: Running Complete Unit Test Suite"
+echo "---------------------------------------------"
+
+echo "🏃 Running all 361 unit tests..."
+python -m pytest tests/ -v
+
+echo "✅ Step 2 Complete: All unit tests passed!"
+echo ""
+
+# Step 3: Final Summary
+echo "🎉 All Code Quality Checks Passed!"
+echo "=================================="
+echo "✅ Linting (ruff): PASSED"
+echo "✅ Formatting (black): PASSED" 
+echo "✅ Import sorting (isort): PASSED"
+echo "✅ Unit tests (361 tests): PASSED"
+echo ""
+echo "🚀 Your code is ready for commit and GitHub Actions!"
+echo "💡 Remember to add simulator tests if you modified tools"