diff --git a/README.md b/README.md
index 9b52871..9c99b3c 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,7 @@ Command-line interface for AI-powered coding tasks. Full details available on th
 - 🔍 **Smart Logging**: Hierarchical, color-coded logging system for clear output
 - 👤 **Human Compatible**: Uses README.md, project files and shell commands to build its own context
 - 🌐 **GitHub Integration**: GitHub mode for working with issues and PRs as part of workflow
+- 📄 **Model Context Protocol**: Support for MCP to access external context sources
 
 Please join the MyCoder.ai discord for support: https://discord.gg/5K6TYrHGHt
 
@@ -36,14 +37,12 @@ mycoder -f prompt.txt
 
 # Disable user prompts for fully automated sessions
 mycoder --userPrompt false "Generate a basic Express.js server"
-# or using the alias
-mycoder --userPrompt false "Generate a basic Express.js server"
 
 # Disable user consent warning and version upgrade check for automated environments
 mycoder --upgradeCheck false "Generate a basic Express.js server"
 
 # Enable GitHub mode via CLI option (overrides config file)
-mycoder --githubMode "Work with GitHub issues and PRs"
+mycoder --githubMode true "Work with GitHub issues and PRs"
 ```
 
 ## Configuration
@@ -99,6 +98,22 @@ export default {
 
   // Base URL configuration (for providers that need it)
   baseUrl: 'http://localhost:11434', // Example for Ollama
+  
+  // MCP configuration
+  mcp: {
+    servers: [
+      {
+        name: 'example',
+        url: 'https://mcp.example.com',
+        auth: {
+          type: 'bearer',
+          token: 'your-token-here',
+        },
+      },
+    ],
+    defaultResources: ['example://docs/api'],
+    defaultTools: ['example://tools/search'],
+  },
 };
 ```
 
@@ -167,4 +182,4 @@ Please see [CONTRIBUTING.md](CONTRIBUTING.md) for details on how to contribute t
 
 ## License
 
-This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
\ No newline at end of file
diff --git a/packages/cli/README.md b/packages/cli/README.md
index d99a941..f0a72de 100644
--- a/packages/cli/README.md
+++ b/packages/cli/README.md
@@ -92,13 +92,27 @@ If GitHub mode is enabled but the requirements are not met, MyCoder will provide
 
 ## Configuration
 
-MyCoder is configured using a `mycoder.config.js` file in your project root, similar to ESLint and other modern JavaScript tools. This file exports a configuration object with your preferred settings.
+MyCoder is configured using a configuration file in your project. MyCoder supports multiple configuration file locations and formats, similar to ESLint and other modern JavaScript tools.
 
-You can create a `mycoder.config.js` file in your project root with your preferred settings.
+### Configuration File Locations
 
-Example configuration file:
+MyCoder will look for configuration in the following locations (in order of precedence):
 
-```javascript
+1. `mycoder.config.js` in your project root
+2. `.mycoder.config.js` in your project root
+3. `.config/mycoder.js` in your project root
+4. `.mycoder.rc` in your project root
+5. `.mycoder.rc` in your home directory
+6. `mycoder` field in `package.json`
+7. `~/.config/mycoder/config.js` (XDG standard user configuration)
+
+Multiple file extensions are supported: `.js`, `.ts`, `.mjs`, `.cjs`, `.json`, `.jsonc`, `.json5`, `.yaml`, `.yml`, and `.toml`.
+
+### Creating a Configuration File
+
+Create a configuration file in your preferred location:
+
+```js
 // mycoder.config.js
 export default {
   // GitHub integration
@@ -116,10 +130,20 @@ export default {
   temperature: 0.7,
 
   // Custom settings
+  // customPrompt can be a string or an array of strings for multiple lines
   customPrompt: '',
+  // Example of multiple line custom prompts:
+  // customPrompt: [
+  //   'Custom instruction line 1',
+  //   'Custom instruction line 2',
+  //   'Custom instruction line 3',
+  // ],
   profile: false,
   tokenCache: true,
 
+  // Base URL configuration (for providers that need it)
+  baseUrl: 'http://localhost:11434', // Example for Ollama
+  
   // MCP configuration
   mcp: {
     servers: [
@@ -133,7 +157,37 @@ export default {
       },
     ],
     defaultResources: ['example://docs/api'],
+    defaultTools: ['example://tools/search'],
   },
+  
+  // Custom commands
+  // Uncomment and modify to add your own commands
+  /*
+  commands: {
+    // Function-based command example
+    "search": {
+      description: "Search for a term in the codebase",
+      args: [
+        { name: "term", description: "Search term", required: true }
+      ],
+      execute: (args) => {
+        return `Find all instances of ${args.term} in the codebase and suggest improvements`;
+      }
+    },
+    
+    // Another example with multiple arguments
+    "fix-issue": {
+      description: "Fix a GitHub issue",
+      args: [
+        { name: "issue", description: "Issue number", required: true },
+        { name: "scope", description: "Scope of the fix", default: "full" }
+      ],
+      execute: (args) => {
+        return `Analyze GitHub issue #${args.issue} and implement a ${args.scope} fix`;
+      }
+    }
+  }
+  */
 };
 ```
 
@@ -168,13 +222,14 @@ export default {
 
 ### Available Configuration Options
 
-- `githubMode`: Enable GitHub mode (requires "gh" cli to be installed) for working with issues and PRs (default: `false`)
+- `githubMode`: Enable GitHub mode (requires "gh" cli to be installed) for working with issues and PRs (default: `true`)
 - `headless`: Run browser in headless mode with no UI showing (default: `true`)
 - `userSession`: Use user's existing browser session instead of sandboxed session (default: `false`)
 - `pageFilter`: Method to process webpage content: 'simple', 'none', or 'readability' (default: `none`)
 - `customPrompt`: Custom instructions to append to the system prompt for both main agent and sub-agents (default: `""`)
 - `tokenCache`: Enable token caching for LLM API calls (default: `true`)
 - `mcp`: Configuration for Model Context Protocol (MCP) integration (default: `{ servers: [], defaultResources: [] }`)
+- `commands`: Custom commands that can be executed via the CLI (default: `{}`)
 
 ### Model Context Protocol (MCP) Configuration
 
@@ -242,26 +297,7 @@ These options are available only as command-line parameters and are not stored i
 - `upgradeCheck`: Disable version upgrade check for automated/remote usage (default: `true`)
 - `userPrompt`: Enable or disable the userPrompt tool (default: `true`)
 
-Example configuration in `mycoder.config.js`:
-
-```js
-// mycoder.config.js
-export default {
-  // Browser settings
-  headless: false, // Show browser UI
-  userSession: true, // Use existing browser session
-  pageFilter: 'readability', // Use readability for webpage processing
-
-  // Custom settings
-  customPrompt:
-    'Always prioritize readability and simplicity in your code. Prefer TypeScript over JavaScript when possible.',
-  tokenCache: false, // Disable token caching for LLM API calls
-
-  // Other configuration options...
-};
-```
-
-You can also set these options via CLI arguments (which will override the config file):
+Example setting these options via CLI arguments (which will override the config file):
 
 ```bash
 # Set browser to show UI for this session only
@@ -275,6 +311,7 @@ mycoder --userSession true "Your prompt here"
 
 - `ANTHROPIC_API_KEY`: Your Anthropic API key (required when using Anthropic models)
 - `OPENAI_API_KEY`: Your OpenAI API key (required when using OpenAI models)
+- `SENTRY_DSN`: Optional Sentry DSN for error tracking
 
 Note: Ollama models do not require an API key as they run locally or on a specified server.
 
@@ -297,4 +334,4 @@ pnpm cli -i
 
 ## License
 
-MIT
+MIT
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