diff --git a/libs/mcp-server/scripts/run_mcp_server.sh b/libs/mcp-server/scripts/run_mcp_server.sh
index e3556b16..d462cae7 100755
--- a/libs/mcp-server/scripts/run_mcp_server.sh
+++ b/libs/mcp-server/scripts/run_mcp_server.sh
@@ -2,59 +2,72 @@
 
 set -e
 
-# Function to check if a command exists
-command_exists() {
-    command -v "$1" >/dev/null 2>&1
-}
+# Redirect all setup and installation output to stderr
+{
+    # Function to check if a command exists
+    command_exists() {
+        command -v "$1" >/dev/null 2>&1
+    }
 
-# Function to check if a Python package is installed
-package_installed() {
-    python3 -c "import importlib.util; print(importlib.util.find_spec('$1') is not None)" | grep -q "True"
-}
+    # Function to check if a Python package is installed
+    package_installed() {
+        python3 -c "import importlib.util; print(importlib.util.find_spec('$1') is not None)" | grep -q "True"
+    }
 
-echo "🚀 CUA MCP Server Setup Script"
-echo "============================="
+    echo "🚀 CUA MCP Server Setup Script"
+    echo "============================="
 
-# Check if Python is installed
-if ! command_exists python3; then
-    echo "❌ Python 3 is not installed. Please install Python 3 and try again."
-    exit 1
-fi
-
-echo "✅ Python 3 is installed"
-
-# Check if pip is installed
-if ! command_exists pip3; then
-    echo "❌ pip3 is not installed. Please install pip and try again."
-    exit 1
-fi
-
-echo "✅ pip3 is installed"
-
-# Check if mcp_server package is installed
-if ! package_installed mcp_server; then
-    echo "🔄 mcp_server package is not installed. Installing now..."
-    pip3 install --user -e .
-    
-    if [ $? -ne 0 ]; then
-        echo "❌ Failed to install mcp_server. Please check the error messages above."
+    # Check if Python is installed
+    if ! command_exists python3; then
+        echo "❌ Python 3 is not installed. Please install Python 3 and try again."
         exit 1
     fi
+
+    echo "✅ Python 3 is installed"
+
+    # Check if pip is installed
+    if ! command_exists pip3; then
+        echo "❌ pip3 is not installed. Please install pip and try again."
+        exit 1
+    fi
+
+    echo "✅ pip3 is installed"
+
+    # Get the directory of this script
+    SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+    PROJECT_ROOT="$(dirname "$(dirname "$SCRIPT_DIR")")"
     
-    echo "✅ mcp_server installed successfully"
-else
-    echo "✅ mcp_server is already installed"
-fi
+    # Add the necessary paths to PYTHONPATH
+    export PYTHONPATH="$PROJECT_ROOT:$PYTHONPATH"
+    
+    # Check if we're in a Python project directory
+    cd "$PROJECT_ROOT"
+    
+    # Check if mcp_server package is installed
+    if ! package_installed mcp_server; then
+        echo "🔄 mcp_server package is not installed. Installing now..."
+        
+        # Check if setup.py or pyproject.toml exists
+        if [ -f "setup.py" ] || [ -f "pyproject.toml" ]; then
+            pip3 install --user -e .
+            
+            if [ $? -ne 0 ]; then
+                echo "❌ Failed to install mcp_server. Please check the error messages above."
+                exit 1
+            fi
+            
+            echo "✅ mcp_server installed successfully"
+        else
+            echo "❌ Cannot install mcp_server: neither setup.py nor pyproject.toml found in $PROJECT_ROOT"
+            # Continue anyway, maybe the module is already in PYTHONPATH
+        fi
+    else
+        echo "✅ mcp_server is already installed"
+    fi
 
-# Run the Python module directly
-echo "🚀 Starting MCP server..."
-
-# Get the directory of this script
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
-PROJECT_ROOT="$(dirname "$(dirname "$SCRIPT_DIR")")"
-
-# Add the necessary paths to PYTHONPATH
-export PYTHONPATH="$PROJECT_ROOT:$PYTHONPATH"
+    echo "🚀 Starting MCP server..."
+} >&2  # Redirect all of the above to stderr
 
+# Only the actual server should communicate on stdout for proper MCP protocol
 # Run the server module directly
-python3 -m mcp_server.server 
\ No newline at end of file
+exec python3 -m mcp_server.server 
\ No newline at end of file