@alcyone-labs/arg-parser 1.0.0 → 1.2.0

package/README.md

@@ -2,37 +2,122 @@
 
 ArgParser is a powerful and flexible library for building command-line interfaces (CLIs) in TypeScript and JavaScript. It helps you define, parse, validate, and handle command-line arguments and sub-commands in a structured, type-safe way.
 
-Whether you're building a simple script or a complex nested CLI application, ArgParser provides the tools to create robust and user-friendly interfaces.
+Whether you're building a simple script, a complex nested CLI application, or an MCP (Model Context Protocol) server, ArgParser provides the tools to create robust and user-friendly interfaces with minimal boilerplate.
 
-## TODOs
+## What's New in v1.2.0
 
-### Features
+### **Critical MCP Fixes & Improvements**
 
-- [] Publish as an open-source library
-- [] Upgrade to Zod/V4
-- [] Add support for locales / translations
-- [] (potentially) support for async type function to enable more flexibility (but at the cost of a potentially much larger issue surface)
-- [] (potentially) add support for fully typed parsed output, this has proven very challenging
+- **Fixed MCP Output Schema Support**: Resolved the critical issue where MCP tools with output schemas failed with `"Tool has an output schema but no structured content was provided"` error
+- **Enhanced Handler Context**: Added `isMcp` flag to handler context, enabling proper MCP mode detection in handlers
+- **Improved Response Format**: MCP tools now correctly return both `content` and `structuredContent` fields as required by the JSON-RPC 2.0 specification
+- **Better Integration**: Handlers can now reliably detect when they're being called from MCP mode vs CLI mode
 
-### (known) Bugs / DX improvement points
+### **What Was Fixed**
+
+**Before v1.2.0**: MCP servers would fail when tools had output schemas defined:
+```
+MCP error -32602: Tool canny-search has an output schema but no structured content was provided
+```
 
-- [] When a flag with `flagOnly: false` is going to consume a value that appears like a valid flag from the set, raise the appropriate warning
-- [] When a flag with `allowMultiple: false` and `flagOnly: true` is passed multiple times (regardless of the options, for example "-1" and later "--one", both being valid), raise the correct error
+**After v1.2.0**: MCP tools with output schemas work correctly, returning proper JSON-RPC 2.0 responses:
+```json
+{
+  "jsonrpc": "2.0",
+  "id": 3,
+  "result": {
+    "content": [{"type": "text", "text": "..."}],
+    "structuredContent": { /* validated against output schema */ }
+  }
+}
+```
+
+### **Handler Context Enhancement**
+
+Handlers now receive an `isMcp` flag to detect execution context:
+
+```typescript
+const cli = ArgParser.withMcp({
+  handler: async (ctx) => {
+    if (ctx.isMcp) {
+      // Running in MCP mode - return structured data
+      return { success: true, data: processedData };
+    } else {
+      // Running in CLI mode - can use console output
+      console.log("Processing complete!");
+      return processedData;
+    }
+  }
+});
+```
+
+## What's New in v1.1.0
+
+### **Major Features**
+
+- **MCP (Model Context Protocol) Integration**: Transform any CLI into an MCP server with multiple transport support. Run MCP servers with stdio, SSE, and HTTP transports simultaneously, including streamable HTTP.
+- **System Flags**: Built-in `--s-debug-print`, `--s-with-env`, `--s-save-to-env`, `--s-enable-fuzzy`, and `--s-save-DXT` for enhanced debugging, configuration, testing, and MCP distribution
+- **Environment Loading**: Load configuration from `.env`, `.yaml`, `.json`, and `.toml` files
+- **Enhanced Debugging**: Comprehensive runtime debugging and configuration export tools
+
+### **Quick Start with MCP**
+
+```typescript
+import { ArgParser } from "@alcyone-labs/arg-parser";
+
+const cli = ArgParser.withMcp({
+  appName: "My CLI Tool",
+  appCommandName: "my-tool",
+  description: "A powerful CLI that can also run as an MCP server",
+  handler: async (ctx) => ({ result: "success", args: ctx.args }),
+})
+.addFlags([
+  { name: "input", options: ["--input", "-i"], type: "string", mandatory: true },
+  { name: "verbose", options: ["--verbose", "-v"], type: "boolean", flagOnly: true },
+])
+.addMcpSubCommand("serve", {
+  name: "my-mcp-server",
+  version: "1.1.0",
+  description: "Expose this CLI as an MCP server",
+}, {
+  // Optional: Configure default transports (CLI flags take precedence)
+  defaultTransports: [
+    { type: "stdio" },
+    { type: "sse", port: 3001, host: "0.0.0.0" }
+  ]
+});
+
+// Use as CLI: my-tool --input data.txt --verbose
+// Use as MCP server with defaults: my-tool serve
+// Use as MCP server with CLI override: my-tool serve --transport sse --port 3002
+// Use with multiple transports: my-tool serve --transports '[{"type":"stdio"},{"type":"sse","port":3001}]'
+```
 
 ## Features
 
-- **Type Safety:** Define expected argument types (string, number, boolean, array, custom functions) and get type-safe parsed results.
-- **Optionally Complex Dynamic Types** Provide a method to trigger arbitrary logic when a flag is encountered and return the output to the parsed flag.
-- **Declarative API:** Configure your CLI structure, flags, and sub-commands using a clear, declarative syntax.
-- **Automatic Help Generation:** Generate comprehensive and contextual help text based on your parser configuration.
-- **Hierarchical Commands:** Easily define nested sub-commands to create complex command structures (e.g., `git commit`, `docker container ls`).
-- **Handler Execution:** Associate handler functions with commands and have them executed automatically upon successful parsing (or manually control execution).
-- **Validation:** Define custom validation rules for flag values.
-- **Conditional Requirements:** Make flags mandatory based on the presence or values of other arguments.
-- **Default Values:** Specify default values for flags if they are not provided on the command line.
-- **Flag Inheritance:** Share common flags between parent and child commands with an intuitive inheritance mechanism.
-- **Error Handling:** Built-in, user-friendly error reporting for common parsing issues, with an option to handle errors manually.
-- **Debugging Tools:** Easily inspect your parser's configuration for complex setups.
+### **Core CLI Features**
+- **Type Safety:** Define expected argument types (string, number, boolean, array, custom functions) and get type-safe parsed results
+- **Declarative API:** Configure your CLI structure, flags, and sub-commands using a clear, declarative syntax
+- **Automatic Help Generation:** Generate comprehensive and contextual help text based on your parser configuration
+- **Hierarchical Commands:** Easily define nested sub-commands to create complex command structures (e.g., `git commit`, `docker container ls`)
+- **Handler Execution:** Associate handler functions with commands and have them executed automatically upon successful parsing
+- **Validation:** Define custom validation rules for flag values with enum support and custom validators
+- **Conditional Requirements:** Make flags mandatory based on the presence or values of other arguments
+- **Default Values:** Specify default values for flags if they are not provided on the command line
+- **Flag Inheritance:** Share common flags between parent and child commands with an intuitive inheritance mechanism
+- **Error Handling:** Built-in, user-friendly error reporting for common parsing issues, with an option to handle errors manually
+
+### **MCP Integration (v1.1.0+)**
+- **Automatic MCP Server Creation:** Transform any CLI into an MCP server with a single method call
+- **Multiple Transport Support:** Run stdio, SSE, and HTTP transports simultaneously on different ports
+- **Type-Safe Tool Generation:** Automatically generate MCP tools with Zod schema validation from CLI definitions
+- **Flexible Configuration:** Support for single transport or complex multi-transport JSON configurations
+
+### **System & Configuration Features (v1.1.0+)**
+- **Environment Loading:** Load configuration from `.env`, `.yaml`, `.json`, and `.toml` files with `--s-with-env`
+- **Configuration Export:** Save current configuration to various formats with `--s-save-to-env`
+- **Advanced Debugging:** Runtime debugging with `--s-debug` and configuration inspection with `--s-debug-print`
+- **CLI Precedence:** Command line arguments always override file configuration
 
 ## Installation
 
@@ -50,8 +135,89 @@ bun add @alcyone-labs/arg-parser
 deno install npm:@alcyone-labs/arg-parser
 ```
 
+### **For MCP Integration (Optional)**
+
+If you plan to use MCP server features, install the additional dependencies:
+
+```bash
+pnpm add @modelcontextprotocol/sdk express
+# or
+npm install @modelcontextprotocol/sdk express
+```
+
+**Note:** MCP dependencies are optional and only required if you use `ArgParser` with MCP features or MCP-related functionality.
+
+## Runtime Compatibility
+
+ArgParser is fully compatible with multiple JavaScript runtimes:
+
+### **BunJS**
+```bash
+# Run TypeScript directly
+bun your-cli.ts --flag value
+
+# Or compile and run
+bun build your-cli.ts --outdir ./dist
+bun ./dist/your-cli.js --flag value
+```
+
+### **Node.js**
+```bash
+# Using tsx for TypeScript
+npx tsx your-cli.ts --flag value
+
+# Using ts-node
+npx ts-node your-cli.ts --flag value
+
+# Or compile and run
+npx tsc your-cli.ts
+node your-cli.js --flag value
+```
+
+### **Deno**
+```bash
+# Run with required permissions
+deno run --unstable-sloppy-imports --allow-read --allow-write --allow-env your-cli.ts --flag value
+
+# Or use the provided deno.json configuration for easier task management
+deno task example:simple-cli --env production --port 8080
+```
+
+### **Using the Library in Your Projects**
+
+Install the library and use it in your projects:
+
+```bash
+# Install the library
+pnpm add @alcyone-labs/arg-parser
+
+# Use in your project
+import { ArgParser } from '@alcyone-labs/arg-parser';
+// or
+const { ArgParser } = require('@alcyone-labs/arg-parser');
+```
+
+### **Running Examples**
+
+Examples are provided as TypeScript source files for educational purposes. Run them directly with your preferred runtime:
+
+```bash
+# BunJS (recommended)
+bun examples/simple-cli.ts --env production --port 8080
+
+# Node.js with tsx
+npx tsx examples/simple-cli.ts --env production --port 8080
+
+# Deno (use predefined tasks)
+deno task example:simple-cli --env production --port 8080
+```
+
+All examples work seamlessly across all three runtimes, ensuring maximum compatibility for your CLI applications.
+
 ## Basic Usage
 
+### **Standard CLI Usage**
+
 Here's a simple example demonstrating how to define flags and parse arguments:
 
 ```typescript
@@ -61,13 +227,15 @@ const parser = new ArgParser({
   appName: "Data Processor",
   appCommandName: "data-proc", // Used in help text and error messages
   description: "A tool for processing data phases",
-  // By default, if a handler is set, it will be executed after successful parsing.
-  // Set handler: () => { ... } here for a root command handler.
+  handler: async (ctx) => {
+    console.log("Processing data with phase:", ctx.args.phase);
+    return { success: true, phase: ctx.args.phase };
+  },
 }).addFlags([
   {
     name: "phase",
     options: ["--phase"],
-    type: String, // Use native types or typeof string equivalents ("string", "number", "boolean", etc.)
+    type: "string", // Use "string", "number", "boolean", or native types
     mandatory: true,
     enum: ["chunking", "pairing", "analysis"],
     description: "Processing phase to execute",
@@ -76,36 +244,133 @@ const parser = new ArgParser({
     name: "batch",
     options: ["-b", "--batch-number"],
     type: "number",
-    mandatory: (args) => args.phase !== "analysis", // Mandatory based on another flag's value
+    mandatory: (args) => args.phase !== "analysis", // Conditional requirement
     defaultValue: 0,
     description: "Batch number (required except for analysis phase)",
   },
   {
     name: "verbose",
-    options: ["-v"],
+    options: ["-v", "--verbose"],
     flagOnly: true, // This flag does not expect a value
     description: "Enable verbose logging",
   },
 ]);
 
-// Parse command line arguments (excluding 'node' and script path)
-// If parsing fails (e.g., missing mandatory flag), ArgParser handles the error
-// by printing a message and exiting (process.exit(1)) by default.
-const args = parser.parse(process.argv.slice(2));
+// Parse and execute
+const result = parser.parse(process.argv.slice(2));
+console.log("Result:", result);
+```
+
+### **MCP Server Usage (v1.1.0+)**
 
-// If parsing succeeds and no command handler was executed,
-// execution continues here with the parsed args.
-console.log("Parsing successful! Arguments:", args);
+Transform your CLI into an MCP server with minimal changes:
 
-// Example of using parsed arguments:
-if (args.phase === "chunking") {
-  if (args.verbose) {
-    console.debug("Starting the chunking phase...");
-  }
-  // Perform chunking logic...
-}
+```typescript
+import { ArgParser } from "@alcyone-labs/arg-parser";
+
+const cli = ArgParser.withMcp({
+  appName: "Data Processor",
+  appCommandName: "data-proc",
+  description: "A tool for processing data phases (CLI + MCP server)",
+  handler: async (ctx) => {
+    console.log("Processing data with phase:", ctx.args.phase);
+    return { success: true, phase: ctx.args.phase, batch: ctx.args.batch };
+  },
+})
+.addFlags([
+  {
+    name: "phase",
+    options: ["--phase"],
+    type: "string",
+    mandatory: true,
+    enum: ["chunking", "pairing", "analysis"],
+    description: "Processing phase to execute",
+  },
+  {
+    name: "batch",
+    options: ["-b", "--batch-number"],
+    type: "number",
+    defaultValue: 0,
+    description: "Batch number for processing",
+  },
+])
+.addMcpSubCommand("serve", {
+  name: "data-processor-mcp",
+  version: "1.1.0",
+  description: "Data Processor MCP Server",
+});
+
+// Use as CLI: data-proc --phase chunking --batch 5
+// Use as MCP server: data-proc serve
+// Use with custom transport: data-proc serve --transport sse --port 3001
+```
+
+## MCP Integration (v1.1.0+)
+
+ArgParser v1.1.0 introduces powerful Model Context Protocol (MCP) integration, allowing you to expose any CLI as an MCP server with minimal code changes.
+
+### **Quick MCP Setup**
+
+1. **Import the MCP-enabled class:**
+   ```typescript
+   import { ArgParser } from "@alcyone-labs/arg-parser";
+   ```
+
+2. **Create your CLI with MCP support:**
+   ```typescript
+   const cli = ArgParser.withMcp({
+     appName: "My Tool",
+     appCommandName: "my-tool",
+     handler: async (ctx) => ({ result: "success", args: ctx.args }),
+   })
+   .addFlags([/* your flags */])
+   .addMcpSubCommand("serve", {
+     name: "my-mcp-server",
+     version: "1.0.0",
+   });
+   ```
+
+3. **Use as CLI or MCP server:**
+   ```bash
+   # CLI usage
+   my-tool --input data.txt --verbose
+
+   # MCP server (stdio)
+   my-tool serve
+
+   # MCP server (HTTP)
+   my-tool serve --transport sse --port 3001
+
+   # Multiple transports
+   my-tool serve --transports '[{"type":"stdio"},{"type":"sse","port":3001}]'
+   ```
+
+### **MCP Transport Options**
+
+- **`stdio`** (default): Standard input/output for CLI tools
+- **`sse`**: Server-Sent Events over HTTP for web applications
+- **`streamable-http`**: HTTP with streaming support for advanced integrations
+
+### **Multiple Transports Simultaneously**
+
+Run multiple transport types at once for maximum flexibility:
+
+```bash
+my-tool serve --transports '[
+  {"type":"stdio"},
+  {"type":"sse","port":3001,"path":"/sse"},
+  {"type":"streamable-http","port":3002,"path":"/mcp","host":"0.0.0.0"}
+]'
 ```
 
+### **Automatic Tool Generation**
+
+Your CLI flags are automatically converted to MCP tools with:
+- **Type-safe schemas** using Zod validation
+- **Automatic documentation** from flag descriptions
+- **Enum validation** for restricted values
+- **Error handling** with detailed messages
+
 ## Core Concepts
 
 ### Defining Flags
@@ -242,6 +507,8 @@ ArgParser excels at building CLIs with nested commands, like `git clone` or `doc
 
 Define sub-commands using the `subCommands` option in the `ArgParser` constructor or the `.addSubCommand(subCommand)` method. Each sub-command requires a `name`, `description`, and a dedicated `ArgParser` instance for its own flags and nested sub-commands.
 
+Note that each flag name set is debounced to make sure there are no duplicates, but the flags are sandboxed within their respective sub-commands. So it's ok to use the same flag on different sub-commands.
+
 ```typescript
 import {
   ArgParser,
@@ -471,9 +738,243 @@ try {
 }
 ```
 
+## Environment Configuration Export
+
+ArgParser includes a built-in system flag `--s-save-to-env` that allows you to export the current parser's configuration and parsed arguments to various file formats. This is useful for creating configuration templates, documenting CLI usage, or generating environment files for deployment.
+
+### Usage
+
+```bash
+# Export to .env format (default for no extension)
+your-cli --flag1 value1 --flag2 --s-save-to-env config.env
+
+# Export to YAML format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.yaml
+
+# Export to JSON format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.json
+
+# Export to TOML format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.toml
+```
+
+### Supported Formats
+
+The format is automatically detected based on the file extension:
+
+- **`.env`** (or no extension): Bash environment variable format
+- **`.yaml` / `.yml`**: YAML format
+- **`.json` / `.jsonc`**: JSON format with metadata
+- **`.toml` / `.tml`**: TOML format
+
+### Behavior
+
+- **Works at any parser level**: Can be used with root commands or sub-commands
+- **Includes inherited flags**: Shows flags from the current parser and all parent parsers in the chain
+- **Comments optional flags**: Flags that are optional and not set are commented out but still documented
+- **Preserves values**: Set flags show their actual values, unset flags show default values or are commented out
+- **Rich documentation**: Each flag includes its description, options, type, and constraints
+
+### Example Output
+
+For a CLI with flags `--verbose`, `--output file.txt`, and `--count 5`:
+
+**`.env` format:**
+```bash
+# Environment configuration generated by ArgParser
+# Format: Bash .env style
+
+# verbose: Enable verbose output
+# Options: -v, --verbose
+# Type: Boolean
+# Default: false
+VERBOSE="true"
+
+# output: Output file path
+# Options: -o, --output
+# Type: String
+OUTPUT="file.txt"
+
+# count: Number of items to process
+# Options: -c, --count
+# Type: Number
+# Default: 10
+COUNT="5"
+```
+
+**`.yaml` format:**
+```yaml
+# Environment configuration generated by ArgParser
+# Format: YAML
+
+# verbose: Enable verbose output
+# Options: -v, --verbose
+# Type: Boolean
+# Default: false
+
+verbose: true
+output: "file.txt"
+count: 5
+```
+
+## System Flags (v1.1.0+)
+
+ArgParser includes several built-in system flags that provide debugging, configuration management, and introspection capabilities. These flags are processed before normal argument parsing and will cause the program to exit after execution.
+
+### **Overview**
+
+System flags use the `--s-*` pattern and provide powerful development and deployment tools:
+
+- **`--s-debug`**: Runtime debugging with step-by-step parsing analysis
+- **`--s-with-env <file>`**: Load configuration from files (`.env`, `.yaml`, `.json`, `.toml`)
+- **`--s-save-to-env <file>`**: Export current configuration to various formats
+- **`--s-debug-print`**: Export complete parser configuration for inspection
+- **`--s-enable-fuzzy`**: Enable fuzzy testing mode (dry-run with no side effects)
+- **`--s-save-DXT [dir]`**: Generate DXT packages for MCP servers (Desktop Extensions)
+
+### `--s-save-to-env <file>`
+
+Exports the current parser's configuration and parsed arguments to various file formats.
+
+```bash
+# Export to .env format (default for no extension)
+your-cli --flag1 value1 --flag2 --s-save-to-env config.env
+
+# Export to YAML format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.yaml
+
+# Export to JSON format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.json
+
+# Export to TOML format
+your-cli --flag1 value1 --flag2 --s-save-to-env config.toml
+```
+
+**Features:**
+- Works at any parser level (root command or sub-commands)
+- Includes inherited flags from parent parsers in the chain
+- Comments out optional flags that are not set
+- Rich documentation for each flag (description, options, type, constraints)
+- Automatic format detection based on file extension
+
+### `--s-with-env <file>`
+
+Loads configuration from a file and merges it with command line arguments. CLI arguments take precedence over file configuration.
+
+```bash
+# Load from .env format (default for no extension)
+your-cli --s-with-env config.env
+
+# Load from YAML format
+your-cli --s-with-env config.yaml
+
+# Load from JSON format
+your-cli --s-with-env config.json
+
+# Load from TOML format
+your-cli --s-with-env config.toml
+
+# Combine with CLI arguments (CLI args override file config)
+your-cli --s-with-env config.yaml --verbose --output override.txt
+```
+
+**Supported Formats:**
+
+The format is automatically detected based on the file extension:
+
+- **`.env`** (or no extension): Dotenv format with `KEY=value` pairs
+- **`.yaml` / `.yml`**: YAML format
+- **`.json` / `.jsonc`**: JSON format (metadata is ignored if present)
+- **`.toml` / `.tml`**: TOML format
+
+**Behavior:**
+
+- **File validation**: Checks if the file exists and can be parsed
+- **Type conversion**: Automatically converts values to match flag types (boolean, number, string, array)
+- **Enum validation**: Validates values against allowed enum options
+- **CLI precedence**: Command line arguments override file configuration
+- **Error handling**: Exits with error code 1 if file cannot be loaded or parsed
+- **Flag matching**: Only loads values for flags that exist in the current parser chain
+
+**Example Configuration Files:**
+
+**.env format:**
+```bash
+VERBOSE=true
+OUTPUT=file.txt
+COUNT=5
+TAGS=tag1,tag2,tag3
+```
+
+**YAML format:**
+```yaml
+verbose: true
+output: file.txt
+count: 5
+tags:
+  - tag1
+  - tag2
+  - tag3
+```
+
+**JSON format:**
+```json
+{
+  "verbose": true,
+  "output": "file.txt",
+  "count": 5,
+  "tags": ["tag1", "tag2", "tag3"]
+}
+```
+
+### `--s-debug-print`
+
+Prints the complete parser configuration to a JSON file and console for debugging complex parser setups.
+
+```bash
+your-cli --s-debug-print
+```
+
+**Output:**
+- Creates `ArgParser.full.json` with the complete parser structure
+- Shows all flags, sub-commands, handlers, and configuration
+- Useful for debugging complex parser hierarchies
+- Human-readable console output with syntax highlighting
+
+### `--s-debug`
+
+Provides detailed runtime debugging information showing how arguments are parsed step-by-step.
+
+```bash
+your-cli --flag1 value1 sub-command --flag2 value2 --s-debug
+```
+
+**Output:**
+- Shows command chain identification process
+- Step-by-step argument parsing simulation
+- Final parser identification
+- Accumulated arguments at each level
+- Remaining arguments after parsing
+- Complete static configuration of the final parser
+
+**Useful for:**
+- Understanding complex command chains
+- Debugging argument parsing issues
+- Seeing how flags are inherited between parsers
+- Troubleshooting sub-command resolution
+
+### Usage Notes
+
+- System flags are processed before normal argument parsing
+- They cause the program to exit after execution (exit code 0 for success)
+- Can be used with any combination of regular flags and sub-commands
+- Particularly useful during development and debugging
+
 ## Debugging
 
-The `printAll(filePath?: string)` method is useful for debugging complex parser configurations. It recursively outputs the structure, options, flags, and handlers of a parser instance and its sub-commands.
+### Programmatic Debugging
+
+The `printAll(filePath?: string)` method is useful for debugging complex parser configurations programmatically. It recursively outputs the structure, options, flags, and handlers of a parser instance and its sub-commands.
 
 - `parser.printAll()`: Prints a colored, human-readable output to the console.
 - `parser.printAll('./config.json')`: Writes the configuration as a pretty-printed JSON file.
@@ -491,13 +992,301 @@ const parser = new ArgParser({ appName: "Debug App" })
 parser.printAll(); // Output to console
 ```
 
+### Runtime Debugging
+
+For runtime debugging, use the system flags documented above:
+
+- `--s-debug-print`: Export complete parser configuration
+- `--s-debug`: Show step-by-step argument parsing process
+- `--s-save-to-env <file>`: Export current configuration to various formats
+- `--s-with-env <file>`: Load configuration from file and merge with CLI arguments
+
+### `--s-enable-fuzzy`
+
+Enables fuzzy testing mode, which acts as a dry-run mode for safe testing without side effects. **No boilerplate code required** - the system automatically prevents CLI execution during fuzzy testing.
+
+```bash
+# Enable fuzzy mode for testing
+your-cli --s-enable-fuzzy --input test.txt --format json
+```
+
+**Features:**
+- **Automatic execution prevention**: No need for complex conditional logic in your CLI code
+- **Zero boilerplate**: Simply export your CLI with `export default cli` and call `cli.parse()`
+- Disables error handling to allow error collection
+- Skips mandatory flag validation for comprehensive testing
+- **Prevents handler function execution** (no side effects)
+- **Logs what each handler would receive** for testing visibility
+- Recursively applies to all subcommand parsers
+- Safe for testing production CLIs with database operations, file modifications, or API calls
+
+**Example Output:**
+```
+[--s-enable-fuzzy] handler() skipped for command chain: (root)
+  Input args: [--s-enable-fuzzy --input test.txt --format json]
+  Parsed args: {"input":"test.txt","format":"json"}
+```
+
+**Use Cases:**
+- Fuzzy testing CLI argument parsing
+- Validating CLI configuration without executing business logic
+- Testing complex command hierarchies safely
+- Automated testing of CLI interfaces
+
+These system flags are particularly useful when you need to debug a CLI application without modifying the source code.
+
+## Fuzzy Testing
+
+ArgParser includes comprehensive fuzzy testing capabilities to automatically test CLI configurations and catch edge cases that manual testing might miss. The fuzzy testing utility systematically explores command paths and generates various flag combinations to ensure robustness.
+
+### **Quick Start**
+
+Test any ArgParser configuration using the built-in fuzzy testing CLI:
+
+```bash
+# Test an ArgParser file
+bun src/fuzzy-test-cli.ts --file examples/getting-started.ts
+
+# Test with custom options and save results
+bun src/fuzzy-test-cli.ts \
+  --file examples/getting-started.ts \
+  --output test-results.json \
+  --format json \
+  --max-depth 3 \
+  --random-tests 20 \
+  --verbose
+```
+
+**Important Note**: Make sure that the `examples/getting-started.ts` file exports the parser instance using `export default` for the fuzzy testing CLI to work correctly.
+
+### **System Flag Integration**
+
+The `--s-enable-fuzzy` system flag makes any CLI fuzzy-test compatible **without any code modifications or boilerplate**:
+
+```bash
+# Enable fuzzy mode for safe testing (dry-run with no side effects)
+your-cli --s-enable-fuzzy --input test.txt --format json
+
+# The fuzzy testing CLI automatically uses this flag
+bun src/fuzzy-test-cli.ts --file your-cli.ts
+```
+
+**Fuzzy mode features:**
+- **Zero boilerplate**: No conditional logic needed - just `export default cli` and `cli.parse()`
+- **Automatic prevention**: System automatically prevents CLI execution during fuzzy testing
+- **Dry-run execution**: Prevents handler function execution (no side effects)
+- **Error collection**: Disables error handling to collect all parsing errors
+- **Argument logging**: Shows what each handler would receive for testing visibility
+- **Safe testing**: Test production CLIs with database operations, file modifications, or API calls
+
+### **Testing Capabilities**
+
+The fuzzy tester automatically tests:
+
+- **Valid combinations**: Proper flag usage with correct types and values
+- **Invalid combinations**: Wrong inputs to verify error handling
+- **Random combinations**: Pseudo-random flag combinations for edge cases
+- **Command paths**: All subcommand combinations up to configurable depth
+- **Performance**: Execution timing for different input complexities
+
+### **Programmatic Usage**
+
+```typescript
+import { ArgParserFuzzyTester } from "@alcyone-labs/arg-parser/fuzzy-tester";
+import { myArgParser } from "./my-cli";
+
+const tester = new ArgParserFuzzyTester(myArgParser, {
+  maxDepth: 5,
+  randomTestCases: 10,
+  includePerformance: true,
+  testErrorCases: true,
+  verbose: false,
+});
+
+const report = await tester.runFuzzyTest();
+console.log(`Success rate: ${(report.successfulTests / report.totalTests * 100).toFixed(1)}%`);
+```
+
+### **Output Formats**
+
+Generate reports in multiple formats:
+
+```bash
+# Human-readable console output
+bun src/fuzzy-test-cli.ts --file my-cli.ts --format text
+
+# Machine-readable JSON
+bun src/fuzzy-test-cli.ts --file my-cli.ts --format json --output results.json
+
+# Documentation-friendly Markdown
+bun src/fuzzy-test-cli.ts --file my-cli.ts --format markdown --output report.md
+```
+
+For complete documentation, examples, and advanced usage patterns, see the [Fuzzy Testing Documentation](docs/fuzzy-testing.md).
+
+### `--s-save-DXT [directory]`
+
+Generates Desktop Extension (DXT) packages for all MCP servers defined in your ArgParser instance. DXT files are zip archives containing a manifest.json and server files, enabling single-click installation of MCP servers in compatible applications like Claude Desktop.
+
+```bash
+# Generate DXT packages in current directory
+your-cli --s-save-DXT
+
+# Generate DXT packages in specific directory
+your-cli --s-save-DXT ./dxt-packages
+
+# Example with multiple MCP servers
+my-tool --s-save-DXT ./extensions
+```
+
+**Features:**
+- **Automatic detection**: Finds all MCP servers added via `addMcpSubCommand()`
+- **Multiple servers**: Generates separate DXT files for each MCP server
+- **Complete tool listing**: Includes all MCP tools in the manifest
+- **Proper metadata**: Uses actual server names, versions, and descriptions
+- **Ready to install**: Generated DXT files work with DXT-compatible applications
+
+**Generated Structure:**
+```
+your-server.dxt (ZIP file)
+├── manifest.json         # Server metadata and tool definitions
+└── server/
+    └── index.js          # Server entry point
+```
+
+**Example Output:**
+```
+🔧 Generating DXT packages for 2 MCP server(s)...
+  ✓ Generated: primary-server.dxt
+    Server: primary-server v1.0.0
+    Tools: 3 tool(s)
+  ✓ Generated: analytics-server.dxt
+    Server: analytics-server v2.1.0
+    Tools: 5 tool(s)
+
+✅ DXT package generation completed!
+Output directory: /path/to/dxt-packages
+```
+
+**Use Cases:**
+- **Distribution**: Package MCP servers for easy sharing and installation
+- **Development**: Create test packages during MCP server development
+- **Deployment**: Generate production-ready DXT files for distribution
+- **Integration**: Prepare MCP servers for Claude Desktop or other DXT-compatible applications
+
+## Changelog
+
+### v1.2.0 (2025-01-02)
+
+**🔧 Critical MCP Fixes & Improvements**
+
+- **Fixed MCP Output Schema Support**: Resolved the critical issue where MCP tools with output schemas failed with `"Tool has an output schema but no structured content was provided"` error
+- **Enhanced Handler Context**: Added `isMcp` flag to handler context for proper MCP mode detection
+- **Improved Response Format**: MCP tools now correctly return both `content` and `structuredContent` fields as required by JSON-RPC 2.0
+- **Better Integration**: Handlers can reliably detect when they're being called from MCP mode vs CLI mode
+
+**What was broken before v1.2.0:**
+- MCP servers would fail when tools had output schemas defined
+- Handlers couldn't reliably detect MCP execution context
+- Response format didn't comply with MCP specification for structured content
+
+**What works now:**
+- ✅ MCP tools with output schemas work correctly
+- ✅ Proper JSON-RPC 2.0 response format with both `content` and `structuredContent`
+- ✅ Handler context includes `isMcp` flag for mode detection
+- ✅ Full compatibility with MCP clients and the Model Context Protocol specification
+
+### v1.1.0 (2024-12-XX)
+
+**Major Features**
+- MCP (Model Context Protocol) Integration with multiple transport support
+- System Flags: `--s-debug-print`, `--s-with-env`, `--s-save-to-env`, `--s-enable-fuzzy`, `--s-save-DXT`
+- Environment Loading from `.env`, `.yaml`, `.json`, and `.toml` files
+- Enhanced Debugging and configuration export tools
+
 ## API Reference
 
 This section provides a quick overview of the main components. See the sections above for detailed explanations and examples.
 
-### `new ArgParser(options?, initialFlags?)`
+### **Core Classes**
+
+#### `ArgParserBase`
+
+Base class providing core CLI parsing functionality without MCP features. Use this for lightweight CLIs that don't need MCP server capabilities.
+
+**Constructor:**
+- `new ArgParserBase(options?, initialFlags?)`: Create basic parser instance
+
+#### `ArgParser` (v1.1.0+)
+
+Main class with built-in MCP server capabilities. Extends `ArgParserBase` with MCP integration.
+
+**Constructors:**
+- `new ArgParser(options?, initialFlags?)`: Create parser with MCP capabilities
+- `ArgParser.withMcp(options?, initialFlags?)`: Factory method for MCP-enabled parser (same as constructor)
+- `ArgParser.fromArgParser(parser)`: Convert existing ArgParserBase to MCP-enabled
+
+**MCP Methods:**
+- `toMcpTools(options?)`: Generate MCP tool structures from CLI definition
+- `createMcpServer(serverInfo, toolOptions?)`: Create MCP server instance
+- `startMcpServer(serverInfo, toolOptions?)`: Start MCP server with stdio transport
+- `startMcpServerWithTransport(serverInfo, transportType, transportOptions?, toolOptions?)`: Start with specific transport
+- `startMcpServerWithMultipleTransports(serverInfo, transports, toolOptions?)`: Start with multiple transports (manual approach)
+- `addMcpSubCommand(name, serverInfo, options?)`: Add MCP server sub-command with optional preset transports (recommended approach)
+- `parse(args, options?)`: Async version supporting async handlers
+
+**MCP Types:**
+- `McpTransportConfig`: Configuration for a single transport (`{ type, port?, host?, path?, sessionIdGenerator? }`)
+- `McpSubCommandOptions`: Options for MCP sub-command (`{ defaultTransport?, defaultTransports?, toolOptions? }`)
+
+**Transport Types:**
+- `"stdio"`: Standard input/output
+- `"sse"`: Server-Sent Events over HTTP
+- `"streamable-http"`: HTTP with streaming support
 
-Constructor for creating a parser instance.
+**Example:**
+```typescript
+const cli = ArgParser.withMcp({
+  appName: "My CLI",
+  handler: async (ctx) => ({ result: ctx.args }),
+})
+.addFlags([/* flags */])
+.addMcpSubCommand("serve", {
+  name: "my-mcp-server",
+  version: "1.0.0",
+});
+
+// Elegant approach: Configure default transports in addMcpSubCommand
+const cli = ArgParser.withMcp({
+  appName: "My Tool",
+  handler: async (ctx) => ({ result: ctx.args }),
+})
+.addFlags([/* your flags */])
+.addMcpSubCommand("serve", {
+  name: "my-server",
+  version: "1.0.0",
+}, {
+  // Default multiple transports - used when no CLI flags provided
+  defaultTransports: [
+    { type: "stdio" },
+    { type: "sse", port: 3001 },
+    { type: "streamable-http", port: 3002 }
+  ]
+});
+
+// Usage: my-tool serve (uses all default transports)
+// Usage: my-tool serve --transports '[{"type":"sse","port":4000}]' (overrides defaults)
+```
+
+### Constructors
+
+#### `new ArgParserBase(options?, initialFlags?)`
+
+Constructor for creating a basic parser instance without MCP capabilities.
+
+#### `new ArgParser(options?, initialFlags?)`
+
+Constructor for creating a parser instance with MCP capabilities.
 
 - `options`: An object (`IArgParserParams`) configuring the parser.
   - `appName?: string`: Display name.
@@ -582,3 +1371,139 @@ Recursively prints the parser configuration.
 - `IParseOptions`: Options for the `parse()` method.
 - `IArgParserParams`: Options for the `ArgParser` constructor.
 - `ArgParserError`: Custom error class thrown on parsing failures when `handleErrors` is `false`.
+
+## Quick Reference
+
+### **Basic CLI Setup**
+```typescript
+import { ArgParser } from "@alcyone-labs/arg-parser";
+
+const cli = new ArgParser({
+  appName: "My Tool",
+  appCommandName: "my-tool",
+  handler: async (ctx) => ({ result: ctx.args }),
+})
+.addFlags([
+  { name: "input", options: ["--input", "-i"], type: "string", mandatory: true },
+  { name: "verbose", options: ["--verbose", "-v"], type: "boolean", flagOnly: true },
+])
+.addSubCommand({
+  name: "process",
+  description: "Process data",
+  handler: async (ctx) => ({ processed: true }),
+  parser: new ArgParser({}, [
+    { name: "format", options: ["--format"], type: "string", enum: ["json", "xml"] },
+  ]),
+});
+```
+
+### **MCP Integration**
+```typescript
+import { ArgParser } from "@alcyone-labs/arg-parser";
+
+const mcpCli = ArgParser.withMcp({ /* same options */ })
+  .addFlags([/* same flags */])
+  .addMcpSubCommand("serve", {
+    name: "my-mcp-server",
+    version: "1.0.0",
+  });
+
+// CLI: my-tool --input data.txt process --format json
+// MCP: my-tool serve --transport sse --port 3001
+```
+
+### **MCP Preset Transport Configuration**
+Configure default transports that will be used when no CLI transport flags are provided:
+
+```typescript
+import { ArgParser, McpTransportConfig } from "@alcyone-labs/arg-parser";
+
+// Single preset transport
+const cliWithPreset = ArgParser.withMcp({
+  appName: "My Tool",
+  handler: async (ctx) => ({ result: ctx.args }),
+})
+.addMcpSubCommand("serve", {
+  name: "my-server",
+  version: "1.0.0",
+}, {
+  defaultTransport: {
+    type: "sse",
+    port: 3001,
+    host: "0.0.0.0"
+  }
+});
+
+// Multiple preset transports
+const cliWithMultiplePresets = ArgParser.withMcp({
+  appName: "Multi-Transport Tool",
+  handler: async (ctx) => ({ result: ctx.args }),
+})
+.addMcpSubCommand("serve", {
+  name: "multi-server",
+  version: "1.0.0",
+}, {
+  defaultTransports: [
+    { type: "stdio" },
+    { type: "sse", port: 3001 },
+    { type: "streamable-http", port: 3002, path: "/api/mcp" }
+  ],
+  toolOptions: {
+    includeSubCommands: true
+  }
+});
+
+// CLI flags always take precedence over presets
+// my-tool serve                    -> Uses preset transports
+// my-tool serve --transport sse    -> Overrides preset with CLI flags
+```
+
+### **System Flags**
+```bash
+# Debug parsing
+my-tool --s-debug --input data.txt process
+
+# Load configuration
+my-tool --s-with-env config.yaml --input override.txt
+
+# Save configuration
+my-tool --input data.txt --s-save-to-env template.yaml
+```
+
+### **Multiple MCP Transports**
+```bash
+# Single transport
+my-tool serve --transport sse --port 3001
+
+# Multiple transports
+my-tool serve --transports '[
+  {"type":"stdio"},
+  {"type":"sse","port":3001},
+  {"type":"streamable-http","port":3002}
+]'
+```
+
+---
+
+**📖 For complete examples and tutorials, see the [`examples/`](./examples/) directory.**
+
+--- 
+
+## Backlog
+
+- [x] Publish as an open-source library
+- [x] Make ArgParser compatible with MCP out-of-the-box
+- [x] Rename --LIB-* flags to --s-*
+- [x] Make it possible to pass a `--s-save-to-env /path/to/file` parameter that saves all the parameters to a file (works with Bash-style .env, JSON, YAML, TOML)
+- [x] Make it possible to pass a `--s-with-env /path/to/file` parameter that loads all the parameters from a file (works with Bash-style .env, JSON, YAML, TOML)
+- [ ] Add System flags to args.systemArgs
+- [ ] Improve flag options collision prevention
+- [ ] Add support for locales / translations
+- [ ] Add support for async type function to enable more flexibility
+- [ ] (potentially) add support for fully typed parsed output, this has proven very challenging
+- [ ] Upgrade to Zod/V4 (V4 does not support functions well, this will take more time, not a priority)
+
+### (known) Bugs / DX improvement points
+
+- [ ] When a flag with `flagOnly: false` is going to consume a value that appears like a valid flag from the set, raise the appropriate warning
+- [ ] When a flag with `allowMultiple: false` and `flagOnly: true` is passed multiple times (regardless of the options, for example "-1" and later "--one", both being valid), raise the correct error