MCP should support .env files

.env files should hold all the secrets and not the mcp_config.json file

Author: NightTrek

.clinerules/mcp_env_configuration.md

@@ -0,0 +1,99 @@
+# Environment Configuration in MCP Servers
+
+## Overview
+Model Context Protocol (MCP) servers often require access to API keys and configuration values that should not be committed to version control. This document outlines the recommended approach for managing environment variables in MCP servers.
+
+## Recommended Implementation
+
+### 1. Project Structure
+Place your `.env` file in the root directory of your MCP server project:
+
+```
+your-mcp-server/
+├── .env              # Environment variables (not committed to git)
+├── .env.example      # Example template (committed to git)
+├── package.json
+└── src/
+    └── ...
+```
+
+### 2. Path Resolution
+When loading the `.env` file, use a reliable path resolution method that works both in development and production:
+
+```typescript
+import * as dotenv from 'dotenv';
+import { fileURLToPath } from 'url';
+import { dirname, resolve } from 'path';
+import * as fs from 'fs';
+
+// Get the directory path for loading the .env file
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+const rootDir = resolve(__dirname, '../..'); // Adjust based on file location
+
+// Load environment variables from .env file
+dotenv.config({ path: resolve(rootDir, '.env') });
+
+// Validate the configuration
+if (fs.existsSync(resolve(rootDir, '.env'))) {
+  console.debug('Environment file loaded successfully');
+} else {
+  console.warn('No .env file found at', resolve(rootDir, '.env'));
+}
+```
+
+### 3. Variable Access
+Use a helper function to safely access required environment variables:
+
+```typescript
+const getRequiredEnv = (key: string): string => {
+  const value = process.env[key];
+  if (!value) {
+    throw new Error(`${key} environment variable is required. Please set it in your configuration.`);
+  }
+  return value;
+};
+
+// Usage
+const apiKey = getRequiredEnv('API_KEY');
+```
+
+### 4. MCP Server Configuration
+When configuring the MCP server in a desktop application like Claude Desktop, provide the environment variables directly:
+
+```json
+{
+  "mcpServers": {
+    "your-mcp-server": {
+      "command": "/path/to/your-mcp-server/build/index.js",
+      "env": {
+        "API_KEY": "your-api-key-here",
+        "OTHER_CONFIG": "other-value"
+      }
+    }
+  }
+}
+```
+
+## Common Issues
+
+### Path Resolution
+- **Issue**: The `.env` file can't be found at runtime
+- **Solution**: Ensure the path is correctly calculated relative to the file location
+- **Debugging**: Add path logging to verify the correct paths are being used
+
+### ES Modules vs CommonJS
+- **Issue**: `require('fs')` not working in ES modules
+- **Solution**: Use `import * as fs from 'fs'` with ES modules
+- **Verification**: Check your `package.json` for `"type": "module"`
+
+### Environment Precedence
+Environment variables from the system take precedence over those in the `.env` file. When debugging, check both sources.
+
+## Best Practices
+
+1. **Never commit** `.env` files to version control
+2. **Always provide** an `.env.example` template
+3. **Validate** required environment variables at startup
+4. **Use path resolution** that works in all environments
+5. **Document** all required environment variables in your README