@alcyone-labs/arg-parser 2.2.1 → 2.3.0

package/dist/index.mjs

@@ -1197,86 +1197,22 @@ function createOutputSchema(pattern2) {
   }
   return OutputSchemaPatterns.successError();
 }
-class DxtGenerator {
-  constructor(argParserInstance) {
+class DxtGeneratorTestUtils {
+  constructor(argParserInstance, extractMcpServerInfo, handleExit) {
     this.argParserInstance = argParserInstance;
-  }
-  /**
-   * Helper method to handle exit logic based on autoExit setting
-   */
-  _handleExit(exitCode, message, type2, data2) {
-    const result = {
-      success: exitCode === 0,
-      exitCode,
-      message,
-      type: type2 || (exitCode === 0 ? "success" : "error"),
-      shouldExit: true,
-      data: data2
-    };
-    if (this.argParserInstance.getAutoExit() && typeof process === "object" && typeof process.exit === "function") {
-      process.exit(exitCode);
-    }
-    return result;
-  }
-  /**
-   * Handles the --s-build-dxt system flag to generate DXT packages for MCP servers
-   */
-  async handleBuildDxtFlag(processArgs, buildDxtIndex) {
-    var _a, _b, _c;
-    try {
-      const isTestMode = process.env["NODE_ENV"] === "test" || ((_a = process.argv[0]) == null ? void 0 : _a.includes("vitest")) || ((_b = process.argv[1]) == null ? void 0 : _b.includes("vitest")) || ((_c = process.argv[1]) == null ? void 0 : _c.includes("tinypool"));
-      if (isTestMode) {
-        return await this.handleTestModeDxtGeneration(
-          processArgs,
-          buildDxtIndex
-        );
-      }
-      const entryPointFile = process.argv[1];
-      if (!entryPointFile || !fs.existsSync(entryPointFile)) {
-        console.error(
-          simpleChalk.red(`Error: Entry point file not found: ${entryPointFile}`)
-        );
-        return this._handleExit(1, "Entry point file not found", "error");
-      }
-      const outputDir = processArgs[buildDxtIndex + 1] || "./dxt";
-      console.log(
-        simpleChalk.cyan(
-          `
-🔧 Building DXT package for entry point: ${path.basename(entryPointFile)}`
-        )
-      );
-      console.log(simpleChalk.gray(`Output directory: ${outputDir}`));
-      await this.buildDxtWithTsdown(entryPointFile, outputDir);
-      console.log(simpleChalk.green(`
-✅ DXT package generation completed!`));
-      return this._handleExit(
-        0,
-        "DXT package generation completed",
-        "success",
-        { entryPoint: entryPointFile, outputDir }
-      );
-    } catch (error) {
-      console.error(
-        simpleChalk.red(
-          `Error generating DXT package: ${error instanceof Error ? error.message : String(error)}`
-        )
-      );
-      return this._handleExit(
-        1,
-        `Error generating DXT package: ${error instanceof Error ? error.message : String(error)}`,
-        "error"
-      );
-    }
+    this.extractMcpServerInfo = extractMcpServerInfo;
+    this.handleExit = handleExit;
   }
   /**
    * Handles DXT generation in test mode by creating mock DXT package structure
+   * This method creates simplified mock files for testing purposes
    */
   async handleTestModeDxtGeneration(processArgs, buildDxtIndex) {
     try {
       const outputDir = processArgs[buildDxtIndex + 1] || "./dxt-packages";
       const mcpTools = this.argParserInstance.toMcpTools();
       if (mcpTools.length === 0) {
-        return this._handleExit(0, "No MCP servers found", "success");
+        return this.handleExit(0, "No MCP servers found", "success");
       }
       const serverInfo = this.extractMcpServerInfo();
       const folderName = `${serverInfo.name.replace(/[^a-zA-Z0-9_-]/g, "_")}-dxt`;
@@ -1332,17 +1268,12 @@ echo "Mock DXT build script for ${serverInfo.name}"`;
         path.join(buildDir, "build-dxt-package.sh"),
         buildScript
       );
-      return this._handleExit(
-        0,
-        "DXT package generation completed",
-        "success",
-        {
-          entryPoint: "test-mode",
-          outputDir: buildDir
-        }
-      );
+      return this.handleExit(0, "DXT package generation completed", "success", {
+        entryPoint: "test-mode",
+        outputDir: buildDir
+      });
     } catch (error) {
-      return this._handleExit(
+      return this.handleExit(
         1,
         `Test mode DXT generation failed: ${error instanceof Error ? error.message : String(error)}`,
         "error"
@@ -1350,96 +1281,155 @@ echo "Mock DXT build script for ${serverInfo.name}"`;
     }
   }
   /**
-   * Generates a DXT package for the unified MCP server
-   * Now supports both withMcp() configuration and legacy addMcpSubCommand()
+   * Checks if the current environment is in test mode
+   * Used to determine whether to use test utilities or production code
    */
-  async generateDxtPackage(mcpSubCommand, outputDir) {
-    const serverInfo = this.extractMcpServerInfo(mcpSubCommand);
-    const tools = this.generateMcpToolsForDxt(mcpSubCommand);
-    const finalOutputDir = outputDir || "./dxt-packages";
-    const folderName = `${serverInfo.name.replace(/[^a-zA-Z0-9_-]/g, "_")}-dxt`;
-    const buildDir = path.join(finalOutputDir, folderName);
-    if (!fs.existsSync(buildDir)) {
-      fs.mkdirSync(buildDir, { recursive: true });
-    }
-    const serverDir = path.join(buildDir, "server");
-    if (!fs.existsSync(serverDir)) {
-      fs.mkdirSync(serverDir, { recursive: true });
-    }
-    const logoFilename = await this.addLogoToFolder(buildDir, serverInfo);
-    const manifest = this.createDxtManifest(
-      serverInfo,
-      tools,
-      mcpSubCommand,
-      logoFilename
-    );
-    this.validateDxtManifest(manifest);
-    fs.writeFileSync(
-      path.join(buildDir, "manifest.json"),
-      JSON.stringify(manifest, null, 2)
-    );
-    this.addOriginalCliToFolder(buildDir);
-    const bundledCliPath = await this.bundleOriginalCliWithTsdown(serverDir);
-    const serverScript = this.createServerScript(serverInfo, bundledCliPath);
-    const serverScriptPath = path.join(serverDir, "index.mjs");
-    fs.writeFileSync(serverScriptPath, serverScript);
-    try {
-      fs.chmodSync(serverScriptPath, 493);
-    } catch (error) {
-      console.warn(
-        "⚠ Could not set executable permission on server script:",
-        error instanceof Error ? error.message : String(error)
-      );
-    }
-    const packageJson = this.createDxtPackageJson(serverInfo);
-    fs.writeFileSync(
-      path.join(buildDir, "package.json"),
-      JSON.stringify(packageJson, null, 2)
-    );
-    const readme = this.createDxtReadme(serverInfo);
-    fs.writeFileSync(path.join(buildDir, "README.md"), readme);
-    const buildScript = this.createSimpleBuildScript(serverInfo);
-    fs.writeFileSync(path.join(buildDir, "build-dxt.sh"), buildScript);
-    const dxtIgnore = this.createDxtIgnore();
-    fs.writeFileSync(path.join(buildDir, ".dxtignore"), dxtIgnore);
-    try {
-      fs.chmodSync(path.join(buildDir, "build-dxt.sh"), 493);
-    } catch (error) {
+  static isTestMode() {
+    var _a, _b, _c;
+    return process.env["NODE_ENV"] === "test" || ((_a = process.argv[0]) == null ? void 0 : _a.includes("vitest")) || ((_b = process.argv[1]) == null ? void 0 : _b.includes("vitest")) || ((_c = process.argv[1]) == null ? void 0 : _c.includes("tinypool"));
+  }
+}
+class DxtGenerator {
+  constructor(argParserInstance) {
+    this.argParserInstance = argParserInstance;
+  }
+  /**
+   * Helper method to handle exit logic based on autoExit setting
+   */
+  _handleExit(exitCode, message, type2, data2) {
+    const result = {
+      success: exitCode === 0,
+      exitCode,
+      message,
+      type: type2 || (exitCode === 0 ? "success" : "error"),
+      shouldExit: true,
+      data: data2
+    };
+    if (this.argParserInstance.getAutoExit() && typeof process === "object" && typeof process.exit === "function") {
+      process.exit(exitCode);
     }
-    console.log(simpleChalk.green(`  ✓ Generated DXT package folder: ${folderName}`));
-    console.log(
-      simpleChalk.gray(`    Server: ${serverInfo.name} v${serverInfo.version}`)
-    );
-    console.log(simpleChalk.gray(`    Tools: ${tools.length} tool(s)`));
-    console.log(simpleChalk.gray(`    Location: ${buildDir}`));
-    console.log(
-      simpleChalk.cyan(`
-📦 Creating DXT package using Anthropic's dxt pack...`)
-    );
-    console.log(simpleChalk.cyan(`
-📋 Manual steps to create your DXT package:`));
-    console.log(simpleChalk.white(`   cd ${path.relative(process.cwd(), buildDir)}`));
-    console.log(simpleChalk.white(`   ./build-dxt.sh`));
+    return result;
   }
   /**
-   * Reads package.json to extract fallback information for DXT manifest
+   * Handles the --s-build-dxt system flag to generate DXT packages for MCP servers
    */
-  readPackageJsonInfo() {
+  async handleBuildDxtFlag(processArgs, buildDxtIndex) {
     try {
-      const packageJsonPath = path.join(process.cwd(), "package.json");
-      if (fs.existsSync(packageJsonPath)) {
-        const packageContent = fs.readFileSync(packageJsonPath, "utf-8");
-        const packageData = JSON.parse(packageContent);
-        return {
-          author: packageData.author,
-          repository: packageData.repository,
-          license: packageData.license,
-          homepage: packageData.homepage
-        };
+      if (DxtGeneratorTestUtils.isTestMode()) {
+        const testUtils = new DxtGeneratorTestUtils(
+          this.argParserInstance,
+          () => this.extractMcpServerInfo(),
+          (exitCode, message, type2, data2) => this._handleExit(exitCode, message, type2, data2)
+        );
+        return await testUtils.handleTestModeDxtGeneration(
+          processArgs,
+          buildDxtIndex
+        );
+      }
+      const withNodeModules = processArgs.includes("--s-with-node-modules");
+      if (withNodeModules) {
+        console.log(
+          simpleChalk.yellow(
+            "🗂️  --s-with-node-modules detected: will include node_modules in bundle"
+          )
+        );
+        const nodeModulesPath = path.resolve("./node_modules");
+        if (!fs.existsSync(nodeModulesPath)) {
+          console.error(
+            simpleChalk.red(
+              "❌ Error: node_modules directory not found. Please run the installation command first."
+            )
+          );
+          console.log(
+            simpleChalk.cyan(
+              "💡 Required command: pnpm install --prod --node-linker=hoisted"
+            )
+          );
+          return this._handleExit(
+            1,
+            "node_modules directory not found",
+            "error"
+          );
+        }
+        try {
+          const nodeModulesContents = fs.readdirSync(nodeModulesPath);
+          const hasNestedNodeModules = nodeModulesContents.filter((item) => !item.startsWith(".") && !item.startsWith("@")).some((item) => {
+            const itemPath = path.join(nodeModulesPath, item);
+            try {
+              return fs.statSync(itemPath).isDirectory() && fs.existsSync(path.join(itemPath, "node_modules"));
+            } catch {
+              return false;
+            }
+          });
+          if (hasNestedNodeModules) {
+            console.warn(
+              simpleChalk.yellow(
+                "⚠️  Warning: Detected nested node_modules. For best results, ensure hoisted installation:"
+              )
+            );
+            console.log(
+              simpleChalk.cyan(
+                "   rm -rf node_modules && pnpm install --prod --node-linker=hoisted"
+              )
+            );
+          } else {
+            console.log(
+              simpleChalk.green(
+                "✅ node_modules appears properly hoisted and ready for bundling"
+              )
+            );
+          }
+        } catch (error) {
+          console.warn(
+            simpleChalk.yellow(
+              `⚠️  Could not validate node_modules structure: ${error instanceof Error ? error.message : String(error)}`
+            )
+          );
+        }
+        console.log(
+          simpleChalk.gray(
+            "💡 This will create a fully autonomous DXT with all native dependencies included"
+          )
+        );
       }
+      const entryPointFile = process.argv[1];
+      if (!entryPointFile || !fs.existsSync(entryPointFile)) {
+        console.error(
+          simpleChalk.red(`Error: Entry point file not found: ${entryPointFile}`)
+        );
+        return this._handleExit(1, "Entry point file not found", "error");
+      }
+      let outputDir = processArgs[buildDxtIndex + 1] || "./dxt";
+      if (outputDir.startsWith("--s-")) outputDir = "./dxt";
+      console.log(
+        simpleChalk.cyan(
+          `
+🔧 Building DXT package for entry point: ${entryPointFile}`
+        )
+      );
+      console.log(simpleChalk.gray(`Output directory: ${outputDir}`));
+      console.log(simpleChalk.gray(`Entrypoint file: ${entryPointFile}`));
+      await this.buildDxtWithTsdown(entryPointFile, outputDir, withNodeModules);
+      console.log(simpleChalk.green(`
+✅ DXT package generation completed!`));
+      return this._handleExit(
+        0,
+        "DXT package generation completed",
+        "success",
+        { entryPoint: entryPointFile, outputDir }
+      );
     } catch (error) {
+      console.error(
+        simpleChalk.red(
+          `Error generating DXT package: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
+      return this._handleExit(
+        1,
+        `Error generating DXT package: ${error instanceof Error ? error.message : String(error)}`,
+        "error"
+      );
     }
-    return null;
   }
   /**
    * Extracts server information from MCP configuration
@@ -1524,518 +1514,9 @@ echo "Mock DXT build script for ${serverInfo.name}"`;
       ];
     }
   }
-  createDxtManifest(serverInfo, tools, mcpSubCommand, logoFilename) {
-    var _a;
-    const packageInfo = this.readPackageJsonInfo();
-    let author = serverInfo.author;
-    if (!author && (packageInfo == null ? void 0 : packageInfo.author)) {
-      if (typeof packageInfo.author === "string") {
-        const match = packageInfo.author.match(/^([^<]+?)(?:\s*<([^>]+)>)?$/);
-        if (match) {
-          author = {
-            name: match[1].trim(),
-            email: (_a = match[2]) == null ? void 0 : _a.trim()
-          };
-        } else {
-          author = { name: packageInfo.author };
-        }
-      } else {
-        author = packageInfo.author;
-      }
-    }
-    if (!author) {
-      throw new Error(
-        "DXT manifest requires author information. Please provide it via withMcp() serverInfo.author, addMcpSubCommand serverInfo.author, or in package.json"
-      );
-    }
-    const cliArgs = this.generateCliArgsForDxt(mcpSubCommand);
-    const { envVars, userConfig } = this.generateEnvAndUserConfig();
-    const manifest = {
-      dxt_version: "0.1",
-      name: serverInfo.name,
-      version: serverInfo.version,
-      description: serverInfo.description || "MCP server generated from ArgParser",
-      author,
-      server: {
-        type: "node",
-        entry_point: "server/index.mjs",
-        mcp_config: {
-          command: "node",
-          args: ["${__dirname}/server/index.mjs", ...cliArgs],
-          env: envVars
-        }
-      },
-      tools: tools.map((tool) => ({
-        name: tool.name,
-        description: tool.description
-      }))
-    };
-    if (logoFilename) {
-      manifest.icon = logoFilename;
-    }
-    if (userConfig && Object.keys(userConfig).length > 0) {
-      manifest.user_config = userConfig;
-    }
-    if (serverInfo.repository || (packageInfo == null ? void 0 : packageInfo.repository)) {
-      manifest.repository = serverInfo.repository || (packageInfo == null ? void 0 : packageInfo.repository);
-    }
-    if (serverInfo.license || (packageInfo == null ? void 0 : packageInfo.license)) {
-      manifest.license = serverInfo.license || (packageInfo == null ? void 0 : packageInfo.license);
-    }
-    if (serverInfo.homepage || (packageInfo == null ? void 0 : packageInfo.homepage)) {
-      manifest.homepage = serverInfo.homepage || (packageInfo == null ? void 0 : packageInfo.homepage);
-    }
-    return manifest;
-  }
-  validateDxtManifest(manifest) {
-    const errors = [];
-    if (!manifest.dxt_version)
-      errors.push("Missing required field: dxt_version");
-    if (!manifest.name) errors.push("Missing required field: name");
-    if (!manifest.version) errors.push("Missing required field: version");
-    if (!manifest.server) errors.push("Missing required field: server");
-    if (!manifest.author) errors.push("Missing required field: author");
-    if (manifest.server) {
-      if (!manifest.server.type)
-        errors.push("Missing required field: server.type");
-      if (!manifest.server.entry_point)
-        errors.push("Missing required field: server.entry_point");
-      if (!manifest.server.mcp_config)
-        errors.push("Missing required field: server.mcp_config");
-      if (manifest.server.mcp_config) {
-        if (!manifest.server.mcp_config.command)
-          errors.push("Missing required field: server.mcp_config.command");
-        if (!manifest.server.mcp_config.args || !Array.isArray(manifest.server.mcp_config.args)) {
-          errors.push(
-            "Missing or invalid field: server.mcp_config.args (must be array)"
-          );
-        }
-      }
-    }
-    if (manifest.author && typeof manifest.author === "object") {
-      if (!manifest.author.name)
-        errors.push("Missing required field: author.name");
-    }
-    if (manifest.dxt_version && manifest.dxt_version !== "0.1") {
-      errors.push("Unsupported dxt_version: only '0.1' is currently supported");
-    }
-    if (errors.length > 0) {
-      throw new Error(
-        `DXT manifest validation failed:
-${errors.map((e) => `  - ${e}`).join("\n")}`
-      );
-    }
-  }
-  createServerScript(serverInfo, bundledCliPath) {
-    const cliImportPath = bundledCliPath || "original-cli.mjs";
-    return `#!/usr/bin/env node
-
-// Generated MCP server for ${serverInfo.name}
-// This server uses @alcyone-labs/arg-parser's built-in MCP functionality for full protocol compliance
-
-// FIRST: Set up MCP-safe logging to prevent STDOUT contamination
-import { createMcpLogger } from '@alcyone-labs/simple-mcp-logger';
-
-// Auto-detect MCP mode and hijack console to prevent protocol corruption
-const mcpLogger = createMcpLogger('${serverInfo.name}');
-globalThis.console = mcpLogger;
-
-// Now import the CLI which already has MCP functionality configured
-import originalCli from './${cliImportPath}';
-
-// Server configuration
-const serverInfo = ${JSON.stringify(serverInfo, null, 2)};
-
-// Use mcpError for debugging output (safe STDERR, visible in client logs)
-console.error(\`MCP Server: \${serverInfo.name} v\${serverInfo.version}\`);
-console.error(\`Description: \${serverInfo.description}\`);
-console.error(\`Generated from @alcyone-labs/arg-parser with built-in MCP functionality\`);
-${bundledCliPath ? "console.error(`Using bundled CLI for autonomous execution`);" : ""}
-
-// The original CLI has MCP functionality configured via withMcp() or addMcpSubCommand()
-// We use the centralized --s-mcp-serve system flag to start the unified MCP server
-
-// Start the MCP server using the library's built-in centralized serving
-// This works with both withMcp() configuration and legacy addMcpSubCommand() setups
-originalCli.parse(['--s-mcp-serve']);
-`;
-  }
-  createDxtPackageJson(serverInfo) {
-    const useLocalBuild = process.env["LOCAL_BUILD"] === "1";
-    const argParserDependency = useLocalBuild ? "file:../../arg-parser-local.tgz" : "^1.3.0";
-    let originalDependencies = {};
-    try {
-      const originalPackageJsonPath = path.join(process.cwd(), "package.json");
-      if (fs.existsSync(originalPackageJsonPath)) {
-        const originalPackageJson = JSON.parse(
-          fs.readFileSync(originalPackageJsonPath, "utf8")
-        );
-        originalDependencies = originalPackageJson.dependencies || {};
-      }
-    } catch (error) {
-      console.warn(
-        "⚠ Could not read original package.json for dependencies:",
-        error instanceof Error ? error.message : String(error)
-      );
-    }
-    const dependencies2 = {
-      ...originalDependencies,
-      "@alcyone-labs/arg-parser": argParserDependency,
-      "@alcyone-labs/simple-mcp-logger": "^1.0.0",
-      "@modelcontextprotocol/sdk": "^1.15.0",
-      zod: "^3.22.4"
-    };
-    const devDependencies = {
-      tsup: "^8.3.5"
-    };
-    Object.keys(dependencies2).forEach((key) => {
-      const depValue = dependencies2[key];
-      if (key !== "@alcyone-labs/arg-parser" && typeof depValue === "string" && depValue.startsWith("file:")) {
-        delete dependencies2[key];
-        console.warn(
-          `⚠ Removed file: dependency ${key} from DXT package (not suitable for distribution)`
-        );
-      }
-    });
-    return {
-      name: serverInfo.name,
-      version: serverInfo.version,
-      description: serverInfo.description,
-      main: "server/index.mjs",
-      type: "module",
-      scripts: {
-        start: "node server/index.mjs",
-        "build-dxt": "./build-dxt.sh"
-      },
-      dependencies: dependencies2,
-      devDependencies,
-      engines: {
-        node: ">=22.0.0"
-      },
-      author: serverInfo.author,
-      license: serverInfo.license || "MIT",
-      repository: serverInfo.repository
-    };
-  }
-  /**
-   * Creates a .dxtignore file to exclude build artifacts and unnecessary files
-   */
-  createDxtIgnore() {
-    return `# DXT ignore file - exclude these files from the DXT package
-# Generated by @alcyone-labs/arg-parser
-
-# Build artifacts and logs
-*.log
-*.tmp
-temp-dxt-build/
-
-# Build scripts (not needed in final package)
-build-dxt.sh
-arg-parser-local.tgz
-tsup.config.autonomous.js
-tsdown.config.mjs
-
-# Original files (replaced by bundled autonomous build)
-server/index.original.mjs
-server/*.autonomous.mjs
-
-# NOTE: server/original-cli.mjs is NOT excluded because it's needed for the MCP server to function
-# The bundled version (if created) will be server/original-cli.bundled.mjs
-
-# NOTE: node_modules/ is NOT excluded because TSDown bundling may not be 100% autonomous
-# If bundling is successful, node_modules won't be needed, but we include it as fallback
-# The bundled server/index.mjs should be fully autonomous and not require node_modules
-
-# Development files
-.git/
-.gitignore
-.env
-.env.*
-
-# OS files
-.DS_Store
-Thumbs.db
-
-# IDE files
-.vscode/
-.idea/
-*.swp
-*.swo
-`;
-  }
-  /**
-   * Creates a simple build script that uses TSDown bundling and Anthropic's dxt pack
-   */
-  createSimpleBuildScript(serverInfo) {
-    return `#!/bin/bash
-
-# Simple DXT Build Script for ${serverInfo.name}
-# Generated by @alcyone-labs/arg-parser with TSDown bundling
-
-set -e
-
-echo "📦 Creating DXT package for ${serverInfo.name}..."
-
-# Step 1: Make server executable (required for MCP)
-echo "🔧 Making server executable..."
-chmod +x server/index.mjs
-
-# Step 2: Handle local development dependencies
-if grep -q "file:.*arg-parser-local.tgz" package.json; then
-  echo "🔧 Checking for local package tarball..."
-
-  # Check if the tarball exists in the parent directory
-  if [ -f "../../arg-parser-local.tgz" ]; then
-    echo "✅ Found local package tarball: ../../arg-parser-local.tgz"
-  else
-    echo "⚠️  Local tarball not found, falling back to npm registry"
-    echo "💡 To use local build, run: cd /path/to/arg-parser && npm pack && cp *.tgz examples/community/canny-cli/"
-
-    # Replace with npm version
-    sed -i.bak 's|"file:.*arg-parser-local.tgz"|"^1.3.0"|g' package.json 2>/dev/null || \\
-      sed -i 's|"file:.*arg-parser-local.tgz"|"^1.3.0"|g' package.json
-  fi
-fi
-
-# Step 3: Install dependencies (for runtime only, bundling was done during generation)
-echo "📦 Installing dependencies..."
-npm install
-
-# Step 4: Validate manifest
-echo "🔍 Validating DXT manifest..."
-if command -v npx >/dev/null 2>&1; then
-  if npx @anthropic-ai/dxt validate manifest.json; then
-    echo "✅ DXT manifest validation passed"
-  else
-    echo "❌ DXT manifest validation failed"
-    exit 1
-  fi
-else
-  echo "⚠️  npx not found, skipping DXT validation"
-fi
-
-# Step 5: Create DXT package using Anthropic's official packer
-echo "📦 Creating DXT package..."
-if command -v npx >/dev/null 2>&1; then
-  # Use dxt pack directly with .dxtignore for clean packaging
-  npx @anthropic-ai/dxt pack . "${serverInfo.name}.dxt"
-else
-  # Fallback to standard zip if npx not available
-  echo "⚠️  npx not found, using zip fallback"
-  zip -r "${serverInfo.name}.dxt" . -x "node_modules/*" "*.log" ".git/*" "build-dxt.sh" "temp-dxt-build/*"
-fi
-
-# Step 6: Sign the DXT package (optional)
-echo "🔐 Signing DXT package..."
-if command -v npx >/dev/null 2>&1 && command -v openssl >/dev/null 2>&1; then
-  if npx @anthropic-ai/dxt sign "${serverInfo.name}.dxt" --self-signed; then
-    echo "✅ DXT package signed successfully"
-  else
-    echo "⚠️  DXT signing failed, but package is still usable"
-  fi
-else
-  echo "⚠️  npx or openssl not found, skipping DXT signing"
-fi
-
-echo "✅ DXT package created: ${serverInfo.name}.dxt"
-echo "🎯 This package includes bundled CLI with all dependencies!"
-echo ""
-echo "🎉 Installation Instructions:"
-echo "You can now take the file '${serverInfo.name}.dxt' and install it on Claude Desktop"
-echo "or supporting applications by using drag & drop on the Extensions Settings page,"
-echo "or directly pointing the file selector to this file."
-echo ""
-echo "📁 DXT file location: $(pwd)/${serverInfo.name}.dxt"
-`;
-  }
-  createDxtReadme(serverInfo) {
-    return `# ${serverInfo.name}
-
-${serverInfo.description}
-
-## Installation
-
-This is a Desktop Extension (DXT) package generated from @alcyone-labs/arg-parser.
-
-### Automatic Installation
-Open this .dxt file with Claude Desktop or other DXT-compatible applications for single-click installation.
-
-### Manual Installation
-1. Extract the .dxt file (it's a ZIP archive)
-2. Run \`npm install\` to install dependencies
-3. Start the server with \`npm start\`
-
-## Tools
-
-This MCP server provides the following tools:
-${this.generateMcpToolsForDxt().map((tool) => `- **${tool.name}**: ${tool.description}`).join("\n")}
-
-## Building DXT Packages
-
-To rebuild the DXT package:
-
-### Prerequisites
-- Node.js 18+ installed
-- npm package manager
-
-### Build Steps
-
-\`\`\`bash
-# 1. Install dependencies
-npm install
-
-# 2. Build DXT package
-npm run build-dxt
-# or
-./build-dxt.sh
-
-# 3. The build script will:
-#    - Install dependencies
-#    - Validate the manifest
-#    - Create the DXT package using Anthropic's official packer
-#    - Sign the package (optional)
-\`\`\`
-
-### Manual Build Process
-
-If the automated build script doesn't work, you can build manually:
-
-\`\`\`bash
-# 1. Install dependencies
-npm install
-
-# 2. Create DXT package
-npx @anthropic-ai/dxt pack . ${serverInfo.name}.dxt
-
-# 2. Update manifest.json
-# Change "entry_point" from "server/index.js" to "dist-autonomous/server.cjs"
-
-# 3. Create new DXT with bundled server
-# Replace server/index.js with dist-autonomous/server.cjs
-# Remove package.json dependencies (optional)
-\`\`\`
-
-### Result
-The resulting DXT package will be completely autonomous and won't require \`npm install\`.
-
-## Generated Information
-
-- **Generator**: @alcyone-labs/arg-parser v1.3.0
-- **Generated**: ${(/* @__PURE__ */ new Date()).toISOString()}
-- **DXT Version**: 0.1
-
-## Note
-
-This is a simplified DXT package. For full functionality and the latest features, use the original CLI directly.
-For autonomous packages, follow the build instructions above.
-`;
-  }
   /**
    * Maps ArgParser flag types to DXT user config types
    */
-  mapFlagTypeToUserConfigType(flagType) {
-    if (typeof flagType === "function") {
-      if (flagType === String) return "string";
-      if (flagType === Number) return "number";
-      if (flagType === Boolean) return "boolean";
-      if (flagType === Array) return "array";
-      if (flagType === Object) return "object";
-      return "string";
-    }
-    switch (String(flagType).toLowerCase()) {
-      case "string":
-        return "string";
-      case "number":
-        return "number";
-      case "boolean":
-        return "boolean";
-      case "table":
-        return "array";
-      case "array":
-        return "array";
-      case "object":
-        return "object";
-      default:
-        return "string";
-    }
-  }
-  /**
-   * Generates CLI arguments for DXT manifest based on ArgParser flags
-   */
-  generateCliArgsForDxt(_mcpSubCommand) {
-    const args = [];
-    args.push("--s-mcp-serve");
-    return args;
-  }
-  /**
-   * Generates environment variables and user config for DXT manifest
-   */
-  generateEnvAndUserConfig() {
-    const envVars = {};
-    const userConfig = {};
-    const flags = this.argParserInstance.flags || [];
-    for (const flag of flags) {
-      const flagName = flag["name"];
-      if (flagName === "help" || flagName === "mcp") continue;
-      if (flag["env"]) {
-        const envVarName = flag["env"];
-        envVars[envVarName] = `\${user_config.${envVarName}}`;
-        userConfig[envVarName] = {
-          type: this.mapFlagTypeToUserConfigType(flag["type"]),
-          title: this.generateUserConfigTitle(envVarName),
-          description: flag["description"] || `${envVarName} environment variable`,
-          required: true,
-          // Always require env vars in user_config for better UX
-          sensitive: this.isSensitiveField(envVarName)
-        };
-      }
-    }
-    if (typeof this.argParserInstance.getTools === "function") {
-      const tools = this.argParserInstance.getTools();
-      for (const [, toolConfig] of tools) {
-        const toolFlags = toolConfig.flags || [];
-        for (const flag of toolFlags) {
-          const flagName = flag["name"];
-          if (flagName === "help" || flagName.startsWith("s-")) continue;
-          if (flag["env"]) {
-            const envVarName = flag["env"];
-            if (!envVars[envVarName]) {
-              envVars[envVarName] = `\${user_config.${envVarName}}`;
-              userConfig[envVarName] = {
-                type: this.mapFlagTypeToUserConfigType(flag["type"]),
-                title: this.generateUserConfigTitle(envVarName),
-                description: flag["description"] || `${envVarName} environment variable`,
-                required: true,
-                // Always require env vars in user_config for better UX
-                sensitive: this.isSensitiveField(envVarName)
-              };
-            }
-          }
-        }
-      }
-    }
-    return { envVars, userConfig };
-  }
-  /**
-   * Generates a user-friendly title for user config fields
-   */
-  generateUserConfigTitle(flagName) {
-    return flagName.split(/[-_]/).map((word) => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase()).join(" ");
-  }
-  /**
-   * Checks if a field should be marked as sensitive in user config
-   */
-  isSensitiveField(fieldName) {
-    const sensitivePatterns = [
-      /key/i,
-      /token/i,
-      /secret/i,
-      /password/i,
-      /auth/i,
-      /credential/i
-    ];
-    return sensitivePatterns.some((pattern2) => pattern2.test(fieldName));
-  }
   /**
    * Adds the logo to the build folder if available
    * @returns The filename of the logo that was added, or undefined if no logo was added
@@ -2055,7 +1536,10 @@ For autonomous packages, follow the build instructions above.
               const urlPath = new URL(customLogo).pathname;
               const urlFilename = path.basename(urlPath);
               if (urlFilename && urlFilename.includes(".")) {
-                logoFilename = urlFilename;
+                const ext = path.extname(urlFilename);
+                logoFilename = `logo${ext}`;
+              } else {
+                logoFilename = "logo.jpg";
               }
               console.log("✓ Downloaded logo from URL");
             } else {
@@ -2082,7 +1566,8 @@ For autonomous packages, follow the build instructions above.
           }
           if (fs.existsSync(logoPath)) {
             logoBuffer = fs.readFileSync(logoPath);
-            logoFilename = path.basename(logoPath);
+            const ext = path.extname(logoPath);
+            logoFilename = `logo${ext}`;
             console.log("✓ Added custom logo from local file");
           } else {
             console.warn(`⚠ Custom logo file not found: ${logoPath}`);
@@ -2111,9 +1596,29 @@ For autonomous packages, follow the build instructions above.
             "logo_1_small.jpg"
           );
         }
+        if (!fs.existsSync(logoPath)) {
+          logoPath = path.join(
+            process.cwd(),
+            "node_modules",
+            "@alcyone-labs",
+            "arg-parser",
+            "dist",
+            "assets",
+            "logo_1_small.jpg"
+          );
+        }
+        if (!fs.existsSync(logoPath)) {
+          logoPath = path.join(
+            process.cwd(),
+            "dist",
+            "assets",
+            "logo_1_small.jpg"
+          );
+        }
         if (fs.existsSync(logoPath)) {
           logoBuffer = fs.readFileSync(logoPath);
-          logoFilename = "logo.jpg";
+          const ext = path.extname(logoPath);
+          logoFilename = `logo${ext}`;
           console.log("✓ Added default logo to build folder");
         } else {
           console.warn(
@@ -2135,317 +1640,82 @@ For autonomous packages, follow the build instructions above.
       return void 0;
     }
   }
-  /**
-   * Processes CLI source code to replace global console with MCP-compliant Logger
-   */
-  processCliSourceForMcp(cliSource) {
-    const consoleReplacement = `import { createMcpLogger } from '@alcyone-labs/arg-parser';
-
-// Replace global console with MCP-compliant logger for DXT packages
-const mcpLogger = createMcpLogger('[CLI]');
-const originalConsole = globalThis.console;
-globalThis.console = {
-  ...originalConsole,
-  log: (...args) => mcpLogger.info(...args),
-  info: (...args) => mcpLogger.info(...args),
-  warn: (...args) => mcpLogger.warn(...args),
-  debug: (...args) => mcpLogger.debug(...args),
-  // Keep error/trace/etc as-is since they use stderr (MCP-compliant)
-  error: originalConsole.error,
-  trace: originalConsole.trace,
-  assert: originalConsole.assert,
-  clear: originalConsole.clear,
-  count: originalConsole.count,
-  countReset: originalConsole.countReset,
-  dir: originalConsole.dir,
-  dirxml: originalConsole.dirxml,
-  group: originalConsole.group,
-  groupCollapsed: originalConsole.groupCollapsed,
-  groupEnd: originalConsole.groupEnd,
-  table: originalConsole.table,
-  time: originalConsole.time,
-  timeEnd: originalConsole.timeEnd,
-  timeLog: originalConsole.timeLog,
-  timeStamp: originalConsole.timeStamp,
-};
-
-`;
-    const lines = cliSource.split("\n");
-    let lastImportIndex = -1;
-    for (let i = 0; i < lines.length; i++) {
-      const line = lines[i].trim();
-      if (line.startsWith("import ") && line.includes("from")) {
-        lastImportIndex = i;
-      } else if (line && !line.startsWith("//") && !line.startsWith("/*") && lastImportIndex >= 0) {
-        break;
-      }
-    }
-    if (lastImportIndex >= 0) {
-      lines.splice(
-        lastImportIndex + 1,
-        0,
-        "",
-        ...consoleReplacement.trim().split("\n")
-      );
-      return lines.join("\n");
-    } else {
-      return consoleReplacement + cliSource;
-    }
-  }
-  /**
-   * Adds the original CLI source to the build folder for handler execution
-   */
-  addOriginalCliToFolder(buildDir) {
-    try {
-      const appCommandName = this.argParserInstance.getAppCommandName();
-      const appName = this.argParserInstance.getAppName();
-      const possibleCliFiles = [
-        // Current working directory common patterns
-        path.join(process.cwd(), "index.js"),
-        path.join(process.cwd(), "index.mjs"),
-        path.join(process.cwd(), "cli.js"),
-        path.join(process.cwd(), "cli.mjs"),
-        path.join(process.cwd(), "main.js"),
-        path.join(process.cwd(), "main.mjs"),
-        // Look for files with the app command name
-        path.join(process.cwd(), `${appCommandName}.js`),
-        path.join(process.cwd(), `${appCommandName}.mjs`),
-        // Look for files with the app command name (sanitized)
-        path.join(
-          process.cwd(),
-          `${appCommandName.replace(/[^a-zA-Z0-9-]/g, "-")}.js`
-        ),
-        path.join(
-          process.cwd(),
-          `${appCommandName.replace(/[^a-zA-Z0-9-]/g, "-")}.mjs`
-        ),
-        // Look for files with app name patterns
-        path.join(
-          process.cwd(),
-          `${appName.toLowerCase().replace(/\s+/g, "-")}-cli.js`
-        ),
-        path.join(
-          process.cwd(),
-          `${appName.toLowerCase().replace(/\s+/g, "-")}-cli.mjs`
-        ),
-        // Look for files with first word of app name + cli
-        path.join(
-          process.cwd(),
-          `${appName.split(" ")[0].toLowerCase()}-cli.js`
-        ),
-        path.join(
-          process.cwd(),
-          `${appName.split(" ")[0].toLowerCase()}-cli.mjs`
-        )
-      ];
-      let cliSourcePath = null;
-      for (const filePath of possibleCliFiles) {
-        if (fs.existsSync(filePath)) {
-          cliSourcePath = filePath;
-          break;
-        }
-      }
-      if (cliSourcePath) {
-        let cliSource = fs.readFileSync(cliSourcePath, "utf8");
-        cliSource = cliSource.replace(
-          /import\s*{\s*([^}]+)\s*}\s*from\s*['"][^'"]*\/dist\/index\.mjs['"];?/g,
-          "import { $1 } from '@alcyone-labs/arg-parser';"
-        );
-        cliSource = cliSource.replace(
-          /import\s+(\w+)\s+from\s*['"][^'"]*\/dist\/index\.mjs['"];?/g,
-          "import $1 from '@alcyone-labs/arg-parser';"
-        );
-        cliSource = this.processCliSourceForMcp(cliSource);
-        const parserVariableMatch = cliSource.match(
-          /const\s+(\w+)\s*=\s*ArgParser\.withMcp\(/
-        );
-        if (parserVariableMatch) {
-          const parserVariable = parserVariableMatch[1];
-          cliSource += `
-
-// Export the parser instance for MCP server use
-export default ${parserVariable};
-
-// Add debugging for main execution
-console.error('[MCP-DEBUG] CLI source loaded, checking execution context...');
-console.error('[MCP-DEBUG] import.meta.url:', import.meta.url);
-console.error('[MCP-DEBUG] process.argv[1]:', process.argv[1]);
-
-// Ensure MCP server processes don't exit prematurely
-console.error('[MCP-DEBUG] Process argv:', process.argv);
-console.error('[MCP-DEBUG] Checking for serve command...');
-
-if (process.argv.includes('serve')) {
-  console.error('[MCP-DEBUG] Detected serve command, setting up MCP server lifecycle...');
-
-  // Override the original parse method to handle async MCP server
-  const originalParse = ${parserVariable}.parse;
-  ${parserVariable}.parse = async function(args) {
-    console.error('[MCP-DEBUG] Starting parse with args:', args);
-
-    try {
-      const result = originalParse.call(this, args);
-      console.error('[MCP-DEBUG] Parse result:', typeof result, result?.constructor?.name);
-
-      // If result is a Promise (MCP server), await it and keep process alive
-      if (result && typeof result.then === 'function') {
-        console.error('[MCP-DEBUG] Detected Promise result, awaiting...');
-        const mcpResult = await result;
-        console.error('[MCP-DEBUG] MCP server started, keeping process alive...');
-
-        // Keep the process alive indefinitely for MCP server
-        const keepAlive = setInterval(() => {
-          // Do nothing, just keep the event loop alive
-        }, 30000);
-
-        // Handle graceful shutdown
-        process.on('SIGINT', () => {
-          console.error('[MCP-INFO] Received SIGINT, shutting down gracefully...');
-          clearInterval(keepAlive);
-          process.exit(0);
-        });
-
-        process.on('SIGTERM', () => {
-          console.error('[MCP-INFO] Received SIGTERM, shutting down gracefully...');
-          clearInterval(keepAlive);
-          process.exit(0);
-        });
-
-        return mcpResult;
-      } else {
-        console.error('[MCP-DEBUG] Non-Promise result, returning normally');
-        return result;
-      }
-    } catch (error) {
-      console.error('[MCP-ERROR] Error in parse:', error);
-      throw error;
-    }
-  };
-}
-`;
-        } else {
-          console.warn(
-            "⚠ Could not find ArgParser instance in CLI source, MCP server may not work properly"
-          );
-        }
-        const serverDir = path.join(buildDir, "server");
-        if (!fs.existsSync(serverDir)) {
-          fs.mkdirSync(serverDir, { recursive: true });
-        }
-        fs.writeFileSync(path.join(serverDir, "original-cli.mjs"), cliSource);
-        console.log(
-          `✓ Added original CLI source to build folder: ${path.basename(cliSourcePath)}`
-        );
-      } else {
-        console.warn(
-          "⚠ Original CLI source not found, handlers may not work properly"
-        );
-        console.warn(
-          "  Searched for:",
-          possibleCliFiles.map((f) => path.basename(f)).join(", ")
-        );
-      }
-    } catch (error) {
-      console.warn(
-        "⚠ Failed to add original CLI source:",
-        error instanceof Error ? error.message : String(error)
-      );
-    }
-  }
   /**
    * Builds a complete DXT package using TSDown CLI for autonomous execution
    */
-  async buildDxtWithTsdown(entryPointFile, outputDir = "./dxt") {
+  async buildDxtWithTsdown(entryPointFile, outputDir = "./dxt", withNodeModules = false) {
     try {
       console.log(simpleChalk.cyan("🔧 Building DXT package with TSDown..."));
-      const entryDir = path.dirname(entryPointFile);
+      const projectRoot = this.findProjectRoot(entryPointFile);
+      const absoluteEntryPath = path.resolve(entryPointFile);
+      const relativeEntryPath = path.relative(projectRoot, absoluteEntryPath);
       const entryFileName = path.basename(entryPointFile);
       console.log(simpleChalk.gray(`Entry point: ${entryPointFile}`));
-      console.log(simpleChalk.gray(`Working directory: ${entryDir}`));
+      console.log(simpleChalk.gray(`Project root: ${projectRoot}`));
+      console.log(simpleChalk.gray(`Relative entry path: ${relativeEntryPath}`));
       const dxtIgnorePath = this.getDxtIgnoreTemplatePath();
       if (fs.existsSync(dxtIgnorePath)) {
-        fs.copyFileSync(dxtIgnorePath, path.join(entryDir, ".dxtignore"));
+        fs.copyFileSync(dxtIgnorePath, path.join(projectRoot, ".dxtignore"));
       }
+      const serverInfo = this.extractMcpServerInfo();
+      const logoFilename = await this.addLogoToFolder(
+        projectRoot,
+        serverInfo,
+        entryPointFile
+      );
+      console.log(
+        logoFilename ? simpleChalk.gray(`✓ Logo prepared: ${logoFilename}`) : simpleChalk.gray("⚠ No logo available")
+      );
       const originalCwd = process.cwd();
       try {
-        process.chdir(entryDir);
+        process.chdir(projectRoot);
         const { build } = await import("tsdown");
-        console.log(simpleChalk.gray(`Building with TSDown: ${entryFileName}`));
+        console.log(simpleChalk.gray(`Building with TSDown: ${relativeEntryPath}`));
+        console.log(
+          simpleChalk.green(
+            `${withNodeModules ? "with node_modules" : "without node_modules"}`
+          )
+        );
         const buildConfig = {
-          entry: [entryFileName],
-          outDir: path.resolve(process.cwd(), outputDir),
-          format: ["esm"],
+          entry: [relativeEntryPath],
+          outDir: path.resolve(originalCwd, outputDir),
+          format: ["es"],
           target: "node22",
-          noExternal: () => true,
+          define: {
+            // Define any compile-time constants
+            NODE_ENV: '"production"'
+          },
           minify: false,
           sourcemap: false,
-          clean: false,
+          // Remove all output folders and artefacts
+          clean: [outputDir, "./.dxtignore", `${outputDir}.dxt`],
           silent: process.env["NO_SILENCE"] !== "1",
-          copy: [
-            // Copy logo from assets - try multiple possible locations
-            ...(() => {
-              const possibleLogoPaths = [
-                // From built library assets
-                path.join(
-                  path.dirname(new URL(import.meta.url).pathname),
-                  "..",
-                  "assets",
-                  "logo_1_small.jpg"
-                ),
-                // From node_modules
-                path.join(
-                  process.cwd(),
-                  "node_modules",
-                  "@alcyone-labs",
-                  "arg-parser",
-                  "dist",
-                  "assets",
-                  "logo_1_small.jpg"
-                ),
-                // From package root dist/assets (for local build)
-                path.join(process.cwd(), "dist", "assets", "logo_1_small.jpg"),
-                // From library root (development)
-                path.join(
-                  process.cwd(),
-                  "..",
-                  "..",
-                  "..",
-                  "docs",
-                  "MCP",
-                  "icons",
-                  "logo_1_small.jpg"
-                )
-              ];
-              for (const logoPath of possibleLogoPaths) {
-                if (fs.existsSync(logoPath)) {
-                  console.log(simpleChalk.gray(`Found logo at: ${logoPath}`));
-                  return [{ from: logoPath, to: "logo.jpg" }];
-                }
-              }
+          external: (_, importer) => withNodeModules ? importer == null ? void 0 : importer.includes("node_modules") : false,
+          noExternal: (_, importer) => withNodeModules ? (importer == null ? void 0 : importer.includes("node_modules")) === false : true,
+          copy: async (options) => {
+            const outputPaths = [
+              "package.json"
+            ];
+            if (withNodeModules) {
               console.log(
-                simpleChalk.yellow("⚠ Logo not found in any expected location")
+                simpleChalk.gray(
+                  "📦 Including node_modules in bundle (may take longer)..."
+                )
               );
-              return [];
-            })()
-          ],
-          external: [
-            // Node.js built-ins only - everything else should be bundled for true autonomy
-            "stream",
-            "fs",
-            "path",
-            "url",
-            "util",
-            "events",
-            "child_process",
-            "os",
-            "tty",
-            "process",
-            "crypto",
-            "http",
-            "https",
-            "net",
-            "zlib"
-          ],
+              outputPaths.push("node_modules");
+            }
+            if (logoFilename) {
+              const logoPath = path.join(process.cwd(), logoFilename);
+              if (fs.existsSync(logoPath)) {
+                console.log(simpleChalk.gray(`Adding logo from: ${logoPath}`));
+                outputPaths.push({
+                  from: logoPath,
+                  to: path.join(options.outDir, logoFilename)
+                });
+              }
+            }
+            return outputPaths;
+          },
           platform: "node",
           plugins: []
         };
@@ -2474,15 +1744,15 @@ export default ${JSON.stringify(buildConfig, null, 2)};
         }
         await build(buildConfig);
         console.log(simpleChalk.green("✅ TSDown bundling completed"));
-        const actualOutputFilename = this.detectTsdownOutputFile(
+        const detectedOutputFile = this.detectTsdownOutputFile(
           outputDir,
           entryFileName
         );
-        await this.copyLogoManually(outputDir);
         await this.setupDxtPackageFiles(
           entryPointFile,
           outputDir,
-          actualOutputFilename ?? void 0
+          detectedOutputFile ?? void 0,
+          logoFilename ?? "logo.jpg"
         );
         console.log(simpleChalk.cyan("📦 DXT package ready for packing"));
         console.log(
@@ -2499,292 +1769,6 @@ export default ${JSON.stringify(buildConfig, null, 2)};
       );
     }
   }
-  /**
-   * Bundles the original CLI using TSDown for autonomous execution (legacy method)
-   */
-  async bundleOriginalCliWithTsdown(serverDir) {
-    try {
-      const { build } = await import("tsdown");
-      console.log(
-        simpleChalk.cyan("🔧 Bundling CLI with TSDown for autonomous execution...")
-      );
-      const configContent = this.getTsdownConfigContent();
-      const localConfigPath = path.join(serverDir, "tsdown.config.mjs");
-      fs.writeFileSync(localConfigPath, configContent);
-      const originalCliPath = path.join(serverDir, "original-cli.mjs");
-      if (!fs.existsSync(originalCliPath)) {
-        console.warn(
-          simpleChalk.yellow("⚠ Original CLI not found, skipping TSDown bundling")
-        );
-        return null;
-      }
-      const buildOptions = {
-        entry: ["original-cli.mjs"],
-        // Use relative path since we'll chdir to serverDir
-        outDir: ".",
-        // Output to current directory (serverDir)
-        format: "esm",
-        target: "node22",
-        // Bundle EVERYTHING except Node.js built-ins for true autonomy
-        noExternal: (id) => {
-          if (!id.startsWith("node:") && !this.isNodeBuiltin(id)) return true;
-          return false;
-        },
-        minify: false,
-        sourcemap: false,
-        clean: false,
-        outExtension: () => ({ js: ".bundled.mjs" }),
-        alias: {
-          // Alias chalk to SimpleChalk for autonomous builds
-          chalk: path.resolve(
-            process.cwd(),
-            "node_modules/@alcyone-labs/arg-parser/dist/SimpleChalk.mjs"
-          )
-        },
-        external: [
-          // Only Node.js built-ins - everything else gets bundled for true autonomy
-          "node:stream",
-          "node:fs",
-          "node:path",
-          "node:url",
-          "node:util",
-          "node:events",
-          "node:child_process",
-          "node:os",
-          "node:tty",
-          "node:process",
-          "node:crypto",
-          "node:http",
-          "node:https",
-          "node:net",
-          "node:zlib",
-          "node:fs/promises",
-          "node:timers",
-          "stream",
-          "fs",
-          "path",
-          "url",
-          "util",
-          "events",
-          "child_process",
-          "os",
-          "tty",
-          "process",
-          "crypto",
-          "http",
-          "https",
-          "net",
-          "zlib",
-          "fs/promises",
-          "timers",
-          "timers/promises",
-          "perf_hooks",
-          "async_hooks",
-          "inspector",
-          "v8",
-          "vm",
-          "assert",
-          "constants",
-          "module",
-          "repl",
-          "string_decoder",
-          "punycode",
-          "domain",
-          "querystring",
-          "readline",
-          "worker_threads",
-          "cluster",
-          "dgram",
-          "dns",
-          "buffer"
-        ],
-        platform: "node",
-        plugins: [],
-        // Resolve local dependencies properly
-        resolve: {
-          alias: {
-            // Handle local monorepo dependencies
-            "@alcyone-labs/arg-parser": path.resolve(process.cwd())
-          }
-        }
-      };
-      const originalCwd = process.cwd();
-      try {
-        process.chdir(serverDir);
-        await build(buildOptions);
-      } finally {
-        process.chdir(originalCwd);
-      }
-      const possibleBundledFiles = [
-        "original-cli.bundled.mjs",
-        "original-cli.js",
-        "original-cli.mjs"
-      ];
-      let bundledPath = null;
-      let bundledFileName = null;
-      for (const fileName of possibleBundledFiles) {
-        const filePath = path.join(serverDir, fileName);
-        if (fs.existsSync(filePath) && fileName !== "original-cli.mjs") {
-          bundledPath = filePath;
-          bundledFileName = fileName;
-          break;
-        }
-      }
-      if (bundledPath && bundledFileName) {
-        console.log(
-          simpleChalk.green(
-            `✅ TSDown bundling completed successfully: ${bundledFileName}`
-          )
-        );
-        const expectedBundledPath = path.join(
-          serverDir,
-          "original-cli.bundled.mjs"
-        );
-        if (bundledPath !== expectedBundledPath) {
-          fs.renameSync(bundledPath, expectedBundledPath);
-          bundledFileName = "original-cli.bundled.mjs";
-        }
-        try {
-          fs.unlinkSync(localConfigPath);
-        } catch (error) {
-        }
-        try {
-          fs.chmodSync(expectedBundledPath, 493);
-        } catch (error) {
-          console.warn(
-            "⚠ Could not set executable permission on bundled file:",
-            error instanceof Error ? error.message : String(error)
-          );
-        }
-        return bundledFileName;
-      } else {
-        console.warn(
-          simpleChalk.yellow("⚠ TSDown bundling failed, bundled file not found")
-        );
-        return null;
-      }
-    } catch (error) {
-      console.warn(
-        simpleChalk.yellow(
-          `⚠ TSDown bundling failed: ${error instanceof Error ? error.message : String(error)}`
-        )
-      );
-      console.log(simpleChalk.gray("  Falling back to non-bundled approach"));
-      return null;
-    }
-  }
-  /**
-   * Checks if a module ID is a Node.js built-in
-   */
-  isNodeBuiltin(id) {
-    const nodeBuiltins = [
-      "stream",
-      "fs",
-      "path",
-      "url",
-      "util",
-      "events",
-      "child_process",
-      "os",
-      "tty",
-      "process",
-      "crypto",
-      "http",
-      "https",
-      "net",
-      "zlib",
-      "fs/promises",
-      "timers",
-      "timers/promises",
-      "perf_hooks",
-      "async_hooks",
-      "inspector",
-      "v8",
-      "vm",
-      "assert",
-      "constants",
-      "module",
-      "repl",
-      "string_decoder",
-      "punycode",
-      "domain",
-      "querystring",
-      "readline",
-      "worker_threads",
-      "cluster",
-      "dgram",
-      "dns",
-      "buffer"
-    ];
-    return nodeBuiltins.includes(id) || id.startsWith("node:");
-  }
-  /**
-   * Gets the TSDown configuration content as a string
-   */
-  getTsdownConfigContent() {
-    const currentDir = path.dirname(new URL(import.meta.url).pathname);
-    const assetsConfigPath = path.join(
-      currentDir,
-      "..",
-      "assets",
-      "tsdown.dxt.config.ts"
-    );
-    if (fs.existsSync(assetsConfigPath)) {
-      try {
-        const content = fs.readFileSync(assetsConfigPath, "utf-8");
-        return content.replace('/// <reference types="tsdown" />', "").replace(
-          'import { defineConfig } from "tsdown/config";',
-          'import { defineConfig } from "tsdown";'
-        ).replace(
-          "export default defineConfig(",
-          "export default defineConfig("
-        );
-      } catch (error) {
-        console.warn(
-          simpleChalk.yellow(
-            "⚠ Could not read TSDown config from assets, using fallback"
-          )
-        );
-      }
-    }
-    const rootConfigPath = path.join(process.cwd(), "tsdown.dxt.config.ts");
-    if (fs.existsSync(rootConfigPath)) {
-      try {
-        const content = fs.readFileSync(rootConfigPath, "utf-8");
-        return content.replace('/// <reference types="tsdown" />', "").replace(
-          'import { defineConfig } from "tsdown/config";',
-          'import { defineConfig } from "tsdown";'
-        );
-      } catch (error) {
-        console.warn(
-          simpleChalk.yellow(
-            "⚠ Could not read TSDown config from root, using default"
-          )
-        );
-      }
-    }
-    return `import { defineConfig } from "tsdown";
-import path from "path";
-
-export default defineConfig({
-  outDir: "server",
-  format: ["esm", "module"],
-  target: "node22",
-  noExternal: () => true,
-  minify: false,
-  sourcemap: false,
-  clean: false,
-  alias: {
-    chalk: path.resolve(process.cwd(), "node_modules/@alcyone-labs/arg-parser/dist/SimpleChalk.mjs"),
-  },
-  external: [
-    "stream", "fs", "path", "url", "util", "events", "child_process",
-    "os", "tty", "process", "crypto", "http", "https", "net", "zlib",
-  ],
-  platform: "node",
-  plugins: [],
-});`;
-  }
   /**
    * Gets the path to the .dxtignore template file in assets
    */
@@ -2824,8 +1808,8 @@ export default defineConfig({
   /**
    * Sets up DXT package files (manifest.json) in the output directory
    */
-  async setupDxtPackageFiles(entryPointFile, outputDir = "./dxt", actualOutputFilename) {
-    var _a, _b, _c, _d, _e;
+  async setupDxtPackageFiles(entryPointFile, outputDir = "./dxt", actualOutputFilename, logoFilename = "logo.jpg") {
+    var _a, _b, _c, _d, _e, _f;
     const dxtDir = path.resolve(process.cwd(), outputDir);
     if (!fs.existsSync(dxtDir)) {
       throw new Error(`TSDown output directory (${outputDir}) not found`);
@@ -2852,10 +1836,10 @@ export default defineConfig({
           `Warning: Could not generate unified tool list: ${error instanceof Error ? error.message : String(error)}`
         )
       );
-      const mainFlags2 = this.argParserInstance.flags;
+      const mainFlags = this.argParserInstance.flags;
       const properties2 = {};
       const required2 = [];
-      for (const flag of mainFlags2) {
+      for (const flag of mainFlags) {
         if (flag.name === "help" || flag.name.startsWith("s-")) continue;
         properties2[flag.name] = {
           type: getJsonSchemaTypeFromFlag(flag.type),
@@ -2879,58 +1863,17 @@ export default defineConfig({
         }
       ];
     }
-    const envVars = {};
-    const userConfig = {};
-    const mainFlags = this.argParserInstance.flags;
-    for (const flag of mainFlags) {
-      const envVar = flag.env || flag.envVar;
-      if (envVar) {
-        envVars[envVar] = `\${user_config.${envVar}}`;
-        userConfig[envVar] = {
-          type: "string",
-          title: envVar.replace(/_/g, " ").replace(/\b\w/g, (l) => l.toUpperCase()),
-          description: flag.description || `${envVar} environment variable`,
-          required: true,
-          // Always require env vars in user_config for better UX
-          sensitive: true
-          // Assume env vars are sensitive
-        };
-      }
-    }
-    if (typeof this.argParserInstance.getTools === "function") {
-      const tools2 = this.argParserInstance.getTools();
-      for (const [, toolConfig] of tools2) {
-        const toolFlags = toolConfig.flags || [];
-        for (const flag of toolFlags) {
-          const envVar = flag.env || flag.envVar;
-          if (envVar && !envVars[envVar]) {
-            envVars[envVar] = `\${user_config.${envVar}}`;
-            userConfig[envVar] = {
-              type: "string",
-              title: envVar.replace(/_/g, " ").replace(/\b\w/g, (l) => l.toUpperCase()),
-              description: flag.description || `${envVar} environment variable`,
-              required: true,
-              // Always require env vars in user_config for better UX
-              sensitive: true
-              // Assume env vars are sensitive
-            };
-          }
-        }
-      }
-    }
+    const { envVars, userConfig } = this.generateEnvAndUserConfig();
     const serverInfo = this.extractMcpServerInfo();
-    let logoFilename = "logo.jpg";
-    if (serverInfo == null ? void 0 : serverInfo.logo) {
-      const customLogoFilename = await this.addLogoToFolder(
-        dxtDir,
-        serverInfo,
-        entryPointFile
-      );
-      if (customLogoFilename) {
-        logoFilename = customLogoFilename;
-      }
+    let entryFileName;
+    if (actualOutputFilename) {
+      entryFileName = actualOutputFilename;
+    } else {
+      const projectRoot = this.findProjectRoot(entryPointFile);
+      const absoluteEntryPath = path.resolve(entryPointFile);
+      const relativeEntryPath = path.relative(projectRoot, absoluteEntryPath);
+      entryFileName = relativeEntryPath.replace(/\.ts$/, ".js");
     }
-    const entryFileName = actualOutputFilename || path.basename(entryPointFile).replace(/\.ts$/, ".js");
     const manifest = {
       dxt_version: "0.1",
       name: serverInfo.name || packageInfo.name || "mcp-server",
@@ -2946,17 +1889,23 @@ export default defineConfig({
         entry_point: entryFileName,
         mcp_config: {
           command: "node",
-          args: [`\${__dirname}/${entryFileName}`, "--s-mcp-serve"],
+          args: [
+            `\${__dirname}/${entryFileName}`,
+            "--s-mcp-serve",
+            // Overwrite the CLI config to only use stdio to avoid conflicts
+            "--s-mcp-transport",
+            "stdio"
+          ],
           env: envVars
         }
       },
       tools,
       icon: logoFilename,
       ...Object.keys(userConfig).length > 0 && { user_config: userConfig },
-      repository: {
+      repository: ((_e = packageInfo.repository) == null ? void 0 : _e.url) ? {
         type: "git",
-        url: ((_e = packageInfo.repository) == null ? void 0 : _e.url) || "https://github.com/alcyone-labs/arg-parser"
-      },
+        url: (_f = packageInfo.repository) == null ? void 0 : _f.url
+      } : void 0,
       license: packageInfo.license || "MIT"
     };
     fs.writeFileSync(
@@ -2965,66 +1914,6 @@ export default defineConfig({
     );
     console.log(simpleChalk.gray("✅ DXT package files set up"));
   }
-  /**
-   * Manually copy logo since TSDown's copy option doesn't work programmatically
-   */
-  async copyLogoManually(outputDir = "./dxt") {
-    const dxtDir = path.resolve(process.cwd(), outputDir);
-    if (!fs.existsSync(dxtDir)) {
-      console.warn(
-        simpleChalk.yellow(
-          `⚠ Output directory (${outputDir}) not found, skipping logo copy`
-        )
-      );
-      return;
-    }
-    const possibleLogoPaths = [
-      // From built library assets
-      path.join(
-        path.dirname(new URL(import.meta.url).pathname),
-        "..",
-        "assets",
-        "logo_1_small.jpg"
-      ),
-      // From node_modules
-      path.join(
-        process.cwd(),
-        "node_modules",
-        "@alcyone-labs",
-        "arg-parser",
-        "dist",
-        "assets",
-        "logo_1_small.jpg"
-      ),
-      // From package root dist/assets (for local build)
-      path.join(process.cwd(), "dist", "assets", "logo_1_small.jpg"),
-      // From library root (development)
-      path.join(
-        process.cwd(),
-        "..",
-        "..",
-        "..",
-        "docs",
-        "MCP",
-        "icons",
-        "logo_1_small.jpg"
-      )
-    ];
-    for (const logoPath of possibleLogoPaths) {
-      if (fs.existsSync(logoPath)) {
-        try {
-          fs.copyFileSync(logoPath, path.join(dxtDir, "logo.jpg"));
-          console.log(simpleChalk.gray(`✅ Logo copied from: ${logoPath}`));
-          return;
-        } catch (error) {
-          console.warn(
-            simpleChalk.yellow(`⚠ Failed to copy logo from ${logoPath}: ${error}`)
-          );
-        }
-      }
-    }
-    console.warn(simpleChalk.yellow("⚠ Logo not found in any expected location"));
-  }
   /**
    * Detects the actual output filename generated by TSDown
    */
@@ -3089,6 +1978,72 @@ export default defineConfig({
       return null;
     }
   }
+  findProjectRoot(entryPointFile) {
+    let currentDir = path.dirname(path.resolve(entryPointFile));
+    let attempts = 0;
+    const maxAttempts = 5;
+    while (attempts < maxAttempts) {
+      const packageJsonPath = path.join(currentDir, "package.json");
+      if (fs.existsSync(packageJsonPath)) {
+        return currentDir;
+      }
+      const parentDir = path.dirname(currentDir);
+      if (parentDir === currentDir) {
+        break;
+      }
+      currentDir = parentDir;
+      attempts++;
+    }
+    throw new Error(
+      `Could not find package.json within ${maxAttempts} directories up from ${entryPointFile}. Please ensure your entry point is within a project that has a package.json file.`
+    );
+  }
+  /**
+   * Generate environment variables and user configuration from ArgParser flags
+   * @returns Object containing envVars and userConfig
+   */
+  generateEnvAndUserConfig() {
+    const envVars = {};
+    const userConfig = {};
+    const mainFlags = this.argParserInstance.flags;
+    for (const flag of mainFlags) {
+      const envVar = flag.env || flag.envVar;
+      if (envVar) {
+        envVars[envVar] = `\${user_config.${envVar}}`;
+        userConfig[envVar] = {
+          type: "string",
+          title: envVar.replace(/_/g, " ").replace(/\b\w/g, (l) => l.toUpperCase()),
+          description: flag.description || `${envVar} environment variable`,
+          required: true,
+          // Always require env vars in user_config for better UX
+          sensitive: true
+          // Assume env vars are sensitive
+        };
+      }
+    }
+    if (typeof this.argParserInstance.getTools === "function") {
+      const tools = this.argParserInstance.getTools();
+      for (const [, toolConfig] of tools) {
+        const toolFlags = toolConfig.flags || [];
+        for (const flag of toolFlags) {
+          const envVar = flag.env || flag.envVar;
+          if (envVar && !envVars[envVar]) {
+            envVars[envVar] = `\${user_config.${envVar}}`;
+            userConfig[envVar] = {
+              type: "string",
+              title: envVar.replace(/_/g, " ").replace(/\b\w/g, (l) => l.toUpperCase()),
+              description: flag.description || `${envVar} environment variable`,
+              required: true,
+              // Always require env vars in user_config for better UX
+              sensitive: true
+              // Assume env vars are sensitive
+            };
+          }
+        }
+      }
+    }
+    return { envVars, userConfig };
+  }
 }
 class McpNotificationsManager {
   constructor() {
@@ -5143,9 +4098,7 @@ _handleMcpServeFlag_fn = async function(processArgs, _mcpServeIndex) {
   const resolvedLogPath = resolveLogPath(effectiveLogPath);
   let mcpLogger;
   try {
-    const mcpLoggerModule = await Function(
-      'return import("@alcyone-labs/simple-mcp-logger")'
-    )();
+    const mcpLoggerModule = await import("@alcyone-labs/simple-mcp-logger");
     mcpLogger = mcpLoggerModule.createMcpLogger("MCP Serve", resolvedLogPath);
     globalThis.console = mcpLogger;
   } catch {
@@ -5256,6 +4209,20 @@ _startUnifiedMcpServer_fn = async function(mcpServerConfig, transportOptions) {
         `Error parsing transports configuration: ${error.message}. Expected JSON format: '[{"type":"stdio"},{"type":"sse","port":3001}]'`
       );
     }
+  } else if (transportOptions.transportType) {
+    const transportType = transportOptions.transportType;
+    const finalTransportOptions = {
+      port: transportOptions.port,
+      host: transportOptions.host || "localhost",
+      path: transportOptions.path || "/mcp"
+    };
+    await mcpParser.startMcpServerWithTransport(
+      serverInfo,
+      transportType,
+      finalTransportOptions,
+      toolOptions,
+      transportOptions.logPath
+    );
   } else if (defaultTransports && defaultTransports.length > 0) {
     await mcpParser.startMcpServerWithMultipleTransports(
       serverInfo,
@@ -5277,16 +4244,10 @@ _startUnifiedMcpServer_fn = async function(mcpServerConfig, transportOptions) {
       transportOptions.logPath
     );
   } else {
-    const transportType = transportOptions.transportType || "stdio";
-    const finalTransportOptions = {
-      port: transportOptions.port,
-      host: transportOptions.host || "localhost",
-      path: transportOptions.path || "/mcp"
-    };
     await mcpParser.startMcpServerWithTransport(
       serverInfo,
-      transportType,
-      finalTransportOptions,
+      "stdio",
+      {},
       toolOptions,
       transportOptions.logPath
     );
@@ -8813,6 +7774,7 @@ class Protocol {
     this._responseHandlers = /* @__PURE__ */ new Map();
     this._progressHandlers = /* @__PURE__ */ new Map();
     this._timeoutInfo = /* @__PURE__ */ new Map();
+    this._pendingDebouncedNotifications = /* @__PURE__ */ new Set();
     this.setNotificationHandler(CancelledNotificationSchema, (notification) => {
       const controller = this._requestHandlerAbortControllers.get(notification.params.requestId);
       controller === null || controller === void 0 ? void 0 : controller.abort(notification.params.reason);
@@ -8894,6 +7856,7 @@ class Protocol {
     const responseHandlers = this._responseHandlers;
     this._responseHandlers = /* @__PURE__ */ new Map();
     this._progressHandlers.clear();
+    this._pendingDebouncedNotifications.clear();
     this._transport = void 0;
     (_a = this.onclose) === null || _a === void 0 ? void 0 : _a.call(this);
     const error = new McpError(ErrorCode.ConnectionClosed, "Connection closed");
@@ -9093,10 +8056,32 @@ class Protocol {
    * Emits a notification, which is a one-way message that does not expect a response.
    */
   async notification(notification, options) {
+    var _a, _b;
     if (!this._transport) {
       throw new Error("Not connected");
     }
     this.assertNotificationCapability(notification.method);
+    const debouncedMethods = (_b = (_a = this._options) === null || _a === void 0 ? void 0 : _a.debouncedNotificationMethods) !== null && _b !== void 0 ? _b : [];
+    const canDebounce = debouncedMethods.includes(notification.method) && !notification.params && !(options === null || options === void 0 ? void 0 : options.relatedRequestId);
+    if (canDebounce) {
+      if (this._pendingDebouncedNotifications.has(notification.method)) {
+        return;
+      }
+      this._pendingDebouncedNotifications.add(notification.method);
+      Promise.resolve().then(() => {
+        var _a2;
+        this._pendingDebouncedNotifications.delete(notification.method);
+        if (!this._transport) {
+          return;
+        }
+        const jsonrpcNotification2 = {
+          ...notification,
+          jsonrpc: "2.0"
+        };
+        (_a2 = this._transport) === null || _a2 === void 0 ? void 0 : _a2.send(jsonrpcNotification2, options).catch((error) => this._onerror(error));
+      });
+      return;
+    }
     const jsonrpcNotification = {
       ...notification,
       jsonrpc: "2.0"