diff --git a/README.md b/README.md
index b56dc30..00396af 100644
--- a/README.md
+++ b/README.md
@@ -741,21 +741,11 @@ Different tools use optimized temperature settings:
 
 **All file paths must be absolute paths.**
 
-### Setup
-1. **Use absolute paths** in all tool calls:
-   ```
-   ✅ "Use gemini to analyze /Users/you/project/src/main.py"
-   ❌ "Use gemini to analyze ./src/main.py"  (will be rejected)
-   ```
-
-2. **Set MCP_PROJECT_ROOT** to your project directory for security:
-   ```json
-   "env": {
-     "GEMINI_API_KEY": "your-key",
-     "MCP_PROJECT_ROOT": "/Users/you/project"
-   }
-   ```
-   The server only allows access to files within this directory.
+When using any Gemini tool, always provide absolute paths:
+```
+✅ "Use gemini to analyze /Users/you/project/src/main.py"
+❌ "Use gemini to analyze ./src/main.py"  (will be rejected)
+```
 
 ## Installation
 
diff --git a/run_gemini.bat b/run_gemini.bat
index 3a7bbd3..ea48f93 100644
--- a/run_gemini.bat
+++ b/run_gemini.bat
@@ -4,6 +4,9 @@ REM Windows batch script to run Gemini MCP server
 REM Get the directory where this script is located
 set SCRIPT_DIR=%~dp0
 
+REM Change to script directory to ensure proper working directory
+cd /d "%SCRIPT_DIR%"
+
 REM Check if virtual environment exists
 if exist "%SCRIPT_DIR%venv\Scripts\activate.bat" (
     REM Activate the virtual environment
diff --git a/run_gemini.sh b/run_gemini.sh
index d8ea5ab..7c6d0df 100755
--- a/run_gemini.sh
+++ b/run_gemini.sh
@@ -15,5 +15,8 @@ else
     PYTHON_EXEC="python3"
 fi
 
+# Change to script directory to ensure proper working directory
+cd "$SCRIPT_DIR"
+
 # Run the server
 exec "$PYTHON_EXEC" "$SCRIPT_DIR/server.py"
\ No newline at end of file
diff --git a/utils/file_utils.py b/utils/file_utils.py
index f562a5f..9b9b411 100644
--- a/utils/file_utils.py
+++ b/utils/file_utils.py
@@ -27,15 +27,23 @@ from .token_utils import estimate_tokens, MAX_CONTEXT_TOKENS
 # Get project root from environment or use current directory
 # This defines the sandbox directory where file access is allowed
 # Security: All file operations are restricted to this directory and its children
-PROJECT_ROOT = Path(os.environ.get("MCP_PROJECT_ROOT", os.getcwd())).resolve()
+default_root = os.environ.get("MCP_PROJECT_ROOT", os.getcwd())
+
+# If current directory is "/" (can happen when launched from Claude Desktop),
+# use the user's home directory as a safe default
+if default_root == "/" or os.getcwd() == "/":
+    default_root = os.path.expanduser("~")
+
+PROJECT_ROOT = Path(default_root).resolve()
 
 # Critical Security Check: Prevent running with overly permissive root
 # Setting PROJECT_ROOT to "/" would allow access to the entire filesystem,
 # which is a severe security vulnerability
 if str(PROJECT_ROOT) == "/":
     raise RuntimeError(
-        "Security Error: MCP_PROJECT_ROOT cannot be set to '/'. "
-        "This would give access to the entire filesystem."
+        "Security Error: PROJECT_ROOT cannot be '/'. "
+        "This would give access to the entire filesystem. "
+        "Please set MCP_PROJECT_ROOT environment variable to a specific directory."
     )