@alcyone-labs/arg-parser 2.2.0 → 2.3.0

package/dist/index.mjs

@@ -284,7 +284,9 @@ class JsonConfigPlugin extends ConfigPlugin {
       const { _meta, ...config } = parsed;
       return config;
     } catch (error) {
-      throw new Error(`Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   generate(_config, flags, parsedArgs) {
@@ -500,7 +502,9 @@ function enableConfigPlugins(pluginNames) {
             globalConfigPluginRegistry.registerPlugin(tomlPlugin);
           }
         } catch (error) {
-          console.warn(`Failed to enable TOML plugin: ${error instanceof Error ? error.message : String(error)}`);
+          console.warn(
+            `Failed to enable TOML plugin: ${error instanceof Error ? error.message : String(error)}`
+          );
         }
         break;
       case "yaml":
@@ -511,7 +515,9 @@ function enableConfigPlugins(pluginNames) {
             globalConfigPluginRegistry.registerPlugin(yamlPlugin);
           }
         } catch (error) {
-          console.warn(`Failed to enable YAML plugin: ${error instanceof Error ? error.message : String(error)}`);
+          console.warn(
+            `Failed to enable YAML plugin: ${error instanceof Error ? error.message : String(error)}`
+          );
         }
         break;
       default:
@@ -535,14 +541,18 @@ class ConfigurationManager {
     } else if (appName && appName !== "Argument Parser") {
       baseName = appName;
     }
-    baseName = baseName.split(/[\s-_]+/).map((word) => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase()).join("");
+    baseName = baseName.split(/[\s-_]+/).map(
+      (word) => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase()
+    ).join("");
     return `${baseName}.env`;
   }
   /**
    * Handles the --s-save-to-env system flag at the final parser level
    */
   handleSaveToEnvFlag(processArgs, parserChain) {
-    const saveToEnvIndex = processArgs.findIndex((arg) => arg === "--s-save-to-env");
+    const saveToEnvIndex = processArgs.findIndex(
+      (arg) => arg === "--s-save-to-env"
+    );
     if (saveToEnvIndex !== -1) {
       let filePath;
       if (saveToEnvIndex + 1 < processArgs.length) {
@@ -568,7 +578,11 @@ class ConfigurationManager {
       const finalParser = parserChain[parserChain.length - 1];
       const parsedArgs = finalParser.getLastParseResult();
       if (!parsedArgs) {
-        console.log(simpleChalk.yellow("No parsed arguments available. Run the command first to generate configuration."));
+        console.log(
+          simpleChalk.yellow(
+            "No parsed arguments available. Run the command first to generate configuration."
+          )
+        );
         return;
       }
       const allFlags = [];
@@ -601,10 +615,18 @@ class ConfigurationManager {
       fs.writeFileSync(filePath, content, "utf8");
       console.log(simpleChalk.green(`✅ Configuration saved to: ${filePath}`));
       console.log(simpleChalk.gray(`Format: ${ext || ".env"}`));
-      console.log(simpleChalk.gray(`Flags saved: ${Object.keys(parsedArgs.args).length}`));
+      console.log(
+        simpleChalk.gray(`Flags saved: ${Object.keys(parsedArgs.args).length}`)
+      );
     } catch (error) {
-      console.error(simpleChalk.red(`❌ Failed to save configuration: ${error instanceof Error ? error.message : String(error)}`));
-      throw new Error(`Failed to save configuration: ${error instanceof Error ? error.message : String(error)}`);
+      console.error(
+        simpleChalk.red(
+          `❌ Failed to save configuration: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
+      throw new Error(
+        `Failed to save configuration: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   /**
@@ -641,7 +663,11 @@ class ConfigurationManager {
       }
       return this.convertConfigToFlagValues(rawConfig, parserChain);
     } catch (error) {
-      console.warn(simpleChalk.yellow(`Warning: Could not load config file ${filePath}: ${error instanceof Error ? error.message : String(error)}`));
+      console.warn(
+        simpleChalk.yellow(
+          `Warning: Could not load config file ${filePath}: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
       return {};
     }
   }
@@ -675,7 +701,9 @@ class ConfigurationManager {
     if (plugin) {
       return plugin.parse(content);
     }
-    console.warn("YAML plugin not available, using simple parser. Install js-yaml and enable YAML plugin for full support.");
+    console.warn(
+      "YAML plugin not available, using simple parser. Install js-yaml and enable YAML plugin for full support."
+    );
     const config = {};
     const lines = content.split("\n");
     let currentKey = null;
@@ -726,7 +754,9 @@ class ConfigurationManager {
     try {
       return JSON.parse(content) || {};
     } catch (error) {
-      throw new Error(`Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to parse JSON: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   /**
@@ -737,7 +767,9 @@ class ConfigurationManager {
     if (plugin) {
       return plugin.parse(content);
     }
-    console.warn("TOML plugin not available, using simple parser. Install smol-toml and enable TOML plugin for full support.");
+    console.warn(
+      "TOML plugin not available, using simple parser. Install smol-toml and enable TOML plugin for full support."
+    );
     const config = {};
     const lines = content.split("\n");
     for (const line of lines) {
@@ -768,13 +800,19 @@ class ConfigurationManager {
     for (const [key, value] of Object.entries(rawConfig)) {
       let flag = allFlags.find((f) => f["name"] === key);
       if (!flag) {
-        flag = allFlags.find((f) => f["name"].toLowerCase() === key.toLowerCase());
+        flag = allFlags.find(
+          (f) => f["name"].toLowerCase() === key.toLowerCase()
+        );
       }
       if (flag) {
         try {
           flagValues[flag["name"]] = this.convertValueToFlagType(value, flag);
         } catch (error) {
-          console.warn(simpleChalk.yellow(`Warning: Could not convert config value for flag '${key}': ${error instanceof Error ? error.message : String(error)}`));
+          console.warn(
+            simpleChalk.yellow(
+              `Warning: Could not convert config value for flag '${key}': ${error instanceof Error ? error.message : String(error)}`
+            )
+          );
         }
       }
     }
@@ -811,17 +849,23 @@ class ConfigurationManager {
       }
       const num = Number(value);
       if (isNaN(num)) {
-        throw new Error(`Cannot convert '${value}' to number for flag '${flag["name"]}'`);
+        throw new Error(
+          `Cannot convert '${value}' to number for flag '${flag["name"]}'`
+        );
       }
       return num;
     } else if (isBooleanType) {
       if (typeof value === "boolean") return value;
       if (typeof value === "string") {
         const lower = value.toLowerCase();
-        if (lower === "true" || lower === "1" || lower === "yes" || lower === "on") return true;
-        if (lower === "false" || lower === "0" || lower === "no" || lower === "off") return false;
+        if (lower === "true" || lower === "1" || lower === "yes" || lower === "on")
+          return true;
+        if (lower === "false" || lower === "0" || lower === "no" || lower === "off")
+          return false;
       }
-      throw new Error(`Cannot convert '${value}' to boolean for flag '${flag["name"]}'`);
+      throw new Error(
+        `Cannot convert '${value}' to boolean for flag '${flag["name"]}'`
+      );
     } else if (flagType === "table") {
       if (Array.isArray(value)) return value;
       if (typeof value === "string") {
@@ -832,13 +876,17 @@ class ConfigurationManager {
           return value.split(",").map((v) => v.trim());
         }
       }
-      throw new Error(`Cannot convert '${value}' to table for flag '${flag["name"]}'`);
+      throw new Error(
+        `Cannot convert '${value}' to table for flag '${flag["name"]}'`
+      );
     } else {
       if (typeof flagType === "function") {
         try {
           return flagType(value);
         } catch (error) {
-          throw new Error(`Custom type conversion failed for flag '${flag["name"]}': ${error instanceof Error ? error.message : String(error)}`);
+          throw new Error(
+            `Custom type conversion failed for flag '${flag["name"]}': ${error instanceof Error ? error.message : String(error)}`
+          );
         }
       }
       return String(value);
@@ -913,7 +961,9 @@ class ConfigurationManager {
         if (Array.isArray(value)) {
           lines.push(`${flag["name"]}:`);
           for (const item of value) {
-            lines.push(`  - ${typeof item === "string" && item.includes(" ") ? `"${item}"` : item}`);
+            lines.push(
+              `  - ${typeof item === "string" && item.includes(" ") ? `"${item}"` : item}`
+            );
           }
         } else if (typeof value === "string" && value.includes(" ")) {
           lines.push(`${flag["name"]}: "${value}"`);
@@ -1147,64 +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`;
@@ -1233,7 +1241,10 @@ class DxtGenerator {
         })),
         icon: "logo.jpg"
       };
-      fs.writeFileSync(path.join(buildDir, "manifest.json"), JSON.stringify(manifest, null, 2));
+      fs.writeFileSync(
+        path.join(buildDir, "manifest.json"),
+        JSON.stringify(manifest, null, 2)
+      );
       const packageJson = {
         name: serverInfo.name,
         version: serverInfo.version,
@@ -1241,7 +1252,10 @@ class DxtGenerator {
         main: "index.mjs",
         type: "module"
       };
-      fs.writeFileSync(path.join(buildDir, "package.json"), JSON.stringify(packageJson, null, 2));
+      fs.writeFileSync(
+        path.join(buildDir, "package.json"),
+        JSON.stringify(packageJson, null, 2)
+      );
       const readme = `# ${serverInfo.name}
 
 ${serverInfo.description}
@@ -1250,88 +1264,172 @@ Generated by @alcyone-labs/arg-parser`;
       fs.writeFileSync(path.join(buildDir, "README.md"), readme);
       const buildScript = `#!/bin/bash
 echo "Mock DXT build script for ${serverInfo.name}"`;
-      fs.writeFileSync(path.join(buildDir, "build-dxt-package.sh"), buildScript);
-      return this._handleExit(0, "DXT package generation completed", "success", {
+      fs.writeFileSync(
+        path.join(buildDir, "build-dxt-package.sh"),
+        buildScript
+      );
+      return this.handleExit(0, "DXT package generation completed", "success", {
         entryPoint: "test-mode",
         outputDir: buildDir
       });
     } catch (error) {
-      return this._handleExit(1, `Test mode DXT generation failed: ${error instanceof Error ? error.message : String(error)}`, "error");
+      return this.handleExit(
+        1,
+        `Test mode DXT generation failed: ${error instanceof Error ? error.message : String(error)}`,
+        "error"
+      );
     }
   }
   /**
-   * Generates a DXT package for the unified MCP server
-   * Now supports both withMcp() configuration and legacy addMcpSubCommand()
+   * Checks if the current environment is in test mode
+   * Used to determine whether to use test utilities or production code
    */
-  async generateDxtPackage(mcpSubCommand, outputDir) {
-    const serverInfo = this.extractMcpServerInfo(mcpSubCommand);
-    const tools = this.generateMcpToolsForDxt(mcpSubCommand);
-    const finalOutputDir = outputDir || "./dxt-packages";
-    const folderName = `${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
@@ -1370,7 +1468,9 @@ echo "Mock DXT build script for ${serverInfo.name}"`;
             toolOptions = mcpConfig.toolOptions;
           }
         }
-        const mcpTools = this.argParserInstance.toMcpTools(toolOptions);
+        const mcpTools = this.argParserInstance.toMcpTools(
+          toolOptions
+        );
         return mcpTools.map((tool) => ({
           name: tool.name,
           description: tool.description
@@ -1394,511 +1494,29 @@ echo "Mock DXT build script for ${serverInfo.name}"`;
           });
         }
       }
-      return tools.length > 0 ? tools : [{
-        name: "main",
-        description: "Main command tool"
-      }];
-    } catch (error) {
-      console.warn(simpleChalk.yellow(`Warning: Could not generate detailed tool list: ${error instanceof Error ? error.message : String(error)}`));
-      return [{
-        name: "main",
-        description: "Main command tool"
-      }];
-    }
-  }
-  createDxtManifest(serverInfo, tools, mcpSubCommand, logoFilename) {
-    var _a;
-    const packageInfo = this.readPackageJsonInfo();
-    let author = serverInfo.author;
-    if (!author && (packageInfo == null ? void 0 : packageInfo.author)) {
-      if (typeof packageInfo.author === "string") {
-        const match = packageInfo.author.match(/^([^<]+?)(?:\s*<([^>]+)>)?$/);
-        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)");
+      return tools.length > 0 ? tools : [
+        {
+          name: "main",
+          description: "Main command tool"
         }
-      }
-    }
-    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)
-              };
-            }
-          }
+      console.warn(
+        simpleChalk.yellow(
+          `Warning: Could not generate detailed tool list: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
+      return [
+        {
+          name: "main",
+          description: "Main command tool"
         }
-      }
+      ];
     }
-    return { envVars, userConfig };
-  }
-  /**
-   * Generates a user-friendly title for user config fields
-   */
-  generateUserConfigTitle(flagName) {
-    return flagName.split(/[-_]/).map((word) => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase()).join(" ");
   }
   /**
-   * Checks if a field should be marked as sensitive in user config
+   * Maps ArgParser flag types to DXT user config types
    */
-  isSensitiveField(fieldName) {
-    const sensitivePatterns = [
-      /key/i,
-      /token/i,
-      /secret/i,
-      /password/i,
-      /auth/i,
-      /credential/i
-    ];
-    return sensitivePatterns.some((pattern2) => pattern2.test(fieldName));
-  }
   /**
    * Adds the logo to the build folder if available
    * @returns The filename of the logo that was added, or undefined if no logo was added
@@ -1918,27 +1536,38 @@ For autonomous packages, follow the build instructions above.
               const urlPath = new URL(customLogo).pathname;
               const urlFilename = path.basename(urlPath);
               if (urlFilename && urlFilename.includes(".")) {
-                logoFilename = urlFilename;
+                const ext = path.extname(urlFilename);
+                logoFilename = `logo${ext}`;
+              } else {
+                logoFilename = "logo.jpg";
               }
               console.log("✓ Downloaded logo from URL");
             } else {
-              console.warn(`⚠ Failed to download logo: HTTP ${response.status}`);
+              console.warn(
+                `⚠ Failed to download logo: HTTP ${response.status}`
+              );
             }
           } catch (error) {
-            console.warn("⚠ Failed to download logo from URL:", error instanceof Error ? error.message : String(error));
+            console.warn(
+              "⚠ Failed to download logo from URL:",
+              error instanceof Error ? error.message : String(error)
+            );
           }
         } else {
           let logoPath;
           if (entryPointFile && !path.isAbsolute(customLogo)) {
             const entryDir = path.dirname(entryPointFile);
             logoPath = path.resolve(entryDir, customLogo);
-            console.log(`📍 Resolving logo path relative to entry point: ${logoPath}`);
+            console.log(
+              `📍 Resolving logo path relative to entry point: ${logoPath}`
+            );
           } else {
             logoPath = path.resolve(customLogo);
           }
           if (fs.existsSync(logoPath)) {
             logoBuffer = fs.readFileSync(logoPath);
-            logoFilename = path.basename(logoPath);
+            const ext = path.extname(logoPath);
+            logoFilename = `logo${ext}`;
             console.log("✓ Added custom logo from local file");
           } else {
             console.warn(`⚠ Custom logo file not found: ${logoPath}`);
@@ -1949,17 +1578,52 @@ For autonomous packages, follow the build instructions above.
         const currentDir = path.dirname(new URL(import.meta.url).pathname);
         let logoPath = path.join(currentDir, "assets", "logo_1_small.jpg");
         if (!fs.existsSync(logoPath)) {
-          logoPath = path.join(currentDir, "..", "docs", "MCP", "icons", "logo_1_small.jpg");
+          logoPath = path.join(
+            currentDir,
+            "..",
+            "docs",
+            "MCP",
+            "icons",
+            "logo_1_small.jpg"
+          );
+        }
+        if (!fs.existsSync(logoPath)) {
+          logoPath = path.join(
+            process.cwd(),
+            "docs",
+            "MCP",
+            "icons",
+            "logo_1_small.jpg"
+          );
         }
         if (!fs.existsSync(logoPath)) {
-          logoPath = path.join(process.cwd(), "docs", "MCP", "icons", "logo_1_small.jpg");
+          logoPath = path.join(
+            process.cwd(),
+            "node_modules",
+            "@alcyone-labs",
+            "arg-parser",
+            "dist",
+            "assets",
+            "logo_1_small.jpg"
+          );
+        }
+        if (!fs.existsSync(logoPath)) {
+          logoPath = path.join(
+            process.cwd(),
+            "dist",
+            "assets",
+            "logo_1_small.jpg"
+          );
         }
         if (fs.existsSync(logoPath)) {
           logoBuffer = fs.readFileSync(logoPath);
-          logoFilename = "logo.jpg";
+          const ext = path.extname(logoPath);
+          logoFilename = `logo${ext}`;
           console.log("✓ Added default logo to build folder");
         } else {
-          console.warn("⚠ No logo found (custom or default), build folder will be created without icon");
+          console.warn(
+            "⚠ No logo found (custom or default), build folder will be created without icon"
+          );
           return void 0;
         }
       }
@@ -1969,260 +1633,89 @@ For autonomous packages, follow the build instructions above.
       }
       return void 0;
     } catch (error) {
-      console.warn("⚠ Failed to add logo to build folder:", error instanceof Error ? error.message : String(error));
+      console.warn(
+        "⚠ Failed to add logo to build folder:",
+        error instanceof Error ? error.message : String(error)
+      );
       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.gray(
+                  "📦 Including node_modules in bundle (may take longer)..."
+                )
+              );
+              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)
+                });
               }
-              console.log(simpleChalk.yellow("⚠ Logo not found in any expected location"));
-              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"
-          ],
+            }
+            return outputPaths;
+          },
           platform: "node",
           plugins: []
         };
@@ -2241,262 +1734,40 @@ export default ${JSON.stringify(buildConfig, null, 2)};
 // To run manually:
 // npx tsdown -c tsdown.config.dxt.ts
 `;
-          fs.writeFileSync(path.join("dxt", "tsdown.config.dxt.ts"), configContent);
-          console.log(simpleChalk.gray("📝 Debug config written to dxt/tsdown.config.dxt.ts"));
+          fs.writeFileSync(
+            path.join("dxt", "tsdown.config.dxt.ts"),
+            configContent
+          );
+          console.log(
+            simpleChalk.gray("📝 Debug config written to dxt/tsdown.config.dxt.ts")
+          );
         }
         await build(buildConfig);
         console.log(simpleChalk.green("✅ TSDown bundling completed"));
-        await this.copyLogoManually(outputDir);
-        await this.setupDxtPackageFiles(entryPointFile, outputDir);
-        console.log(simpleChalk.cyan("📦 DXT package ready for packing"));
-        console.log(simpleChalk.gray(`To complete the process, run: npx @anthropic-ai/dxt pack ${outputDir}/`));
-      } finally {
-        process.chdir(originalCwd);
-      }
-    } catch (error) {
-      throw new Error(`TSDown DXT build failed: ${error instanceof Error ? error.message : String(error)}`);
-    }
-  }
-  /**
-   * 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);
+        const detectedOutputFile = this.detectTsdownOutputFile(
+          outputDir,
+          entryFileName
+        );
+        await this.setupDxtPackageFiles(
+          entryPointFile,
+          outputDir,
+          detectedOutputFile ?? void 0,
+          logoFilename ?? "logo.jpg"
+        );
+        console.log(simpleChalk.cyan("📦 DXT package ready for packing"));
+        console.log(
+          simpleChalk.gray(
+            `To complete the process, run: npx @anthropic-ai/dxt pack ${outputDir}/`
+          )
+        );
       } 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"));
-      }
+      throw new Error(
+        `TSDown DXT build failed: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
-    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
@@ -2504,9 +1775,22 @@ export default defineConfig({
   getDxtIgnoreTemplatePath() {
     const possiblePaths = [
       // 1. From the built library assets (when installed via npm)
-      path.join(path.dirname(new URL(import.meta.url).pathname), "..", "assets", ".dxtignore.template"),
+      path.join(
+        path.dirname(new URL(import.meta.url).pathname),
+        "..",
+        "assets",
+        ".dxtignore.template"
+      ),
       // 2. From node_modules/@alcyone-labs/arg-parser/dist/assets (when installed via npm)
-      path.join(process.cwd(), "node_modules", "@alcyone-labs", "arg-parser", "dist", "assets", ".dxtignore.template"),
+      path.join(
+        process.cwd(),
+        "node_modules",
+        "@alcyone-labs",
+        "arg-parser",
+        "dist",
+        "assets",
+        ".dxtignore.template"
+      ),
       // 3. From the root directory (development/local build)
       path.join(process.cwd(), ".dxtignore.template"),
       // 4. From the library root (when using local file dependency)
@@ -2524,8 +1808,8 @@ export default defineConfig({
   /**
    * Sets up DXT package files (manifest.json) in the output directory
    */
-  async setupDxtPackageFiles(entryPointFile, outputDir = "./dxt") {
-    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`);
@@ -2547,11 +1831,15 @@ export default defineConfig({
         description: tool.description
       }));
     } catch (error) {
-      console.warn(simpleChalk.yellow(`Warning: Could not generate unified tool list: ${error instanceof Error ? error.message : String(error)}`));
-      const mainFlags2 = this.argParserInstance.flags;
+      console.warn(
+        simpleChalk.yellow(
+          `Warning: Could not generate unified tool list: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
+      const mainFlags = this.argParserInstance.flags;
       const properties2 = {};
       const required2 = [];
-      for (const flag of mainFlags2) {
+      for (const flag of mainFlags) {
         if (flag.name === "help" || flag.name.startsWith("s-")) continue;
         properties2[flag.name] = {
           type: getJsonSchemaTypeFromFlag(flag.type),
@@ -2568,59 +1856,24 @@ export default defineConfig({
         }
       }
       const commandName = this.argParserInstance.getAppCommandName();
-      tools = [{
-        name: commandName || packageInfo.name || "cli-tool",
-        description: packageInfo.description || this.argParserInstance.getDescription() || "CLI tool"
-      }];
-    }
-    const envVars = {};
-    const userConfig = {};
-    const mainFlags = this.argParserInstance.flags;
-    for (const flag of mainFlags) {
-      const envVar = flag.env || flag.envVar;
-      if (envVar) {
-        envVars[envVar] = `\${user_config.${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 || `${envVar} environment variable`,
-              required: true,
-              // Always require env vars in user_config for better UX
-              sensitive: true
-              // Assume env vars are sensitive
-            };
-          }
+      tools = [
+        {
+          name: commandName || packageInfo.name || "cli-tool",
+          description: packageInfo.description || this.argParserInstance.getDescription() || "CLI tool"
         }
-      }
+      ];
     }
+    const { envVars, userConfig } = this.generateEnvAndUserConfig();
     const serverInfo = this.extractMcpServerInfo();
-    let logoFilename = "logo.jpg";
-    if (serverInfo == null ? void 0 : serverInfo.logo) {
-      const customLogoFilename = await this.addLogoToFolder(dxtDir, serverInfo, entryPointFile);
-      if (customLogoFilename) {
-        logoFilename = customLogoFilename;
-      }
+    let entryFileName;
+    if (actualOutputFilename) {
+      entryFileName = actualOutputFilename;
+    } else {
+      const projectRoot = this.findProjectRoot(entryPointFile);
+      const absoluteEntryPath = path.resolve(entryPointFile);
+      const relativeEntryPath = path.relative(projectRoot, absoluteEntryPath);
+      entryFileName = relativeEntryPath.replace(/\.ts$/, ".js");
     }
-    const entryFileName = path.basename(entryPointFile);
     const manifest = {
       dxt_version: "0.1",
       name: serverInfo.name || packageInfo.name || "mcp-server",
@@ -2638,7 +1891,10 @@ export default defineConfig({
           command: "node",
           args: [
             `\${__dirname}/${entryFileName}`,
-            "--s-mcp-serve"
+            "--s-mcp-serve",
+            // Overwrite the CLI config to only use stdio to avoid conflicts
+            "--s-mcp-transport",
+            "stdio"
           ],
           env: envVars
         }
@@ -2646,46 +1902,147 @@ export default defineConfig({
       tools,
       icon: logoFilename,
       ...Object.keys(userConfig).length > 0 && { user_config: userConfig },
-      repository: {
+      repository: ((_e = packageInfo.repository) == null ? void 0 : _e.url) ? {
         type: "git",
-        url: ((_e = packageInfo.repository) == null ? void 0 : _e.url) || "https://github.com/alcyone-labs/arg-parser"
-      },
+        url: (_f = packageInfo.repository) == null ? void 0 : _f.url
+      } : void 0,
       license: packageInfo.license || "MIT"
     };
-    fs.writeFileSync(path.join(dxtDir, "manifest.json"), JSON.stringify(manifest, null, 2));
+    fs.writeFileSync(
+      path.join(dxtDir, "manifest.json"),
+      JSON.stringify(manifest, null, 2)
+    );
     console.log(simpleChalk.gray("✅ DXT package files set up"));
   }
   /**
-   * Manually copy logo since TSDown's copy option doesn't work programmatically
+   * Detects the actual output filename generated by TSDown
    */
-  async copyLogoManually(outputDir = "./dxt") {
-    const dxtDir = path.resolve(process.cwd(), outputDir);
-    if (!fs.existsSync(dxtDir)) {
-      console.warn(simpleChalk.yellow(`⚠ Output directory (${outputDir}) not found, skipping logo copy`));
-      return;
+  detectTsdownOutputFile(outputDir, expectedBaseName) {
+    try {
+      const dxtDir = path.resolve(process.cwd(), outputDir);
+      if (!fs.existsSync(dxtDir)) {
+        console.warn(
+          simpleChalk.yellow(`⚠ Output directory (${outputDir}) not found`)
+        );
+        return null;
+      }
+      const files = fs.readdirSync(dxtDir).filter(
+        (file) => (file.endsWith(".js") || file.endsWith(".mjs")) && !file.includes("chunk-") && !file.includes("dist-") && !file.startsWith(".")
+      );
+      const baseNameWithoutExt = path.parse(expectedBaseName).name;
+      for (const ext of [".js", ".mjs"]) {
+        const exactMatch = `${baseNameWithoutExt}${ext}`;
+        if (files.includes(exactMatch)) {
+          console.log(simpleChalk.gray(`✓ Detected TSDown output: ${exactMatch}`));
+          return exactMatch;
+        }
+      }
+      const mainFiles = files.filter(
+        (file) => !file.includes("chunk") && !file.includes("dist") && file !== "logo.jpg" && file !== "manifest.json"
+      );
+      if (mainFiles.length === 1) {
+        console.log(simpleChalk.gray(`✓ Detected TSDown output: ${mainFiles[0]}`));
+        return mainFiles[0];
+      }
+      if (mainFiles.length > 1) {
+        let bestMatch = mainFiles[0];
+        let bestScore = 0;
+        for (const file of mainFiles) {
+          const filePath = path.join(dxtDir, file);
+          const stats = fs.statSync(filePath);
+          const nameScore = file.includes(baseNameWithoutExt) ? 100 : 0;
+          const sizeScore = Math.min(stats.size / 1e3, 50);
+          const totalScore = nameScore + sizeScore;
+          if (totalScore > bestScore) {
+            bestScore = totalScore;
+            bestMatch = file;
+          }
+        }
+        console.log(
+          simpleChalk.gray(
+            `✓ Detected TSDown output: ${bestMatch} (best match from ${mainFiles.length} candidates)`
+          )
+        );
+        return bestMatch;
+      }
+      console.warn(
+        simpleChalk.yellow(`⚠ Could not detect TSDown output file in ${outputDir}`)
+      );
+      return null;
+    } catch (error) {
+      console.warn(
+        simpleChalk.yellow(
+          `⚠ Error detecting TSDown output: ${error instanceof Error ? error.message : String(error)}`
+        )
+      );
+      return null;
     }
-    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}`));
+  }
+  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 || `${envVar} environment variable`,
+              required: true,
+              // Always require env vars in user_config for better UX
+              sensitive: true
+              // Assume env vars are sensitive
+            };
+          }
         }
       }
     }
-    console.warn(simpleChalk.yellow("⚠ Logo not found in any expected location"));
+    return { envVars, userConfig };
   }
 }
 class McpNotificationsManager {
@@ -2840,10 +2197,16 @@ class McpNotificationsManager {
   sendNotificationToClient(client, type2) {
     try {
       if (client.connection && typeof client.connection.sendNotification === "function") {
-        client.connection.sendNotification(`notifications/${type2}/list_changed`, {});
+        client.connection.sendNotification(
+          `notifications/${type2}/list_changed`,
+          {}
+        );
       }
     } catch (error) {
-      console.error(`Error sending notification to client ${client.clientId}:`, error);
+      console.error(
+        `Error sending notification to client ${client.clientId}:`,
+        error
+      );
       this.removeClient(client.clientId);
     }
   }
@@ -2932,7 +2295,9 @@ class McpPromptsManager {
       return await entry.config.handler(validatedArgs);
     } catch (error) {
       if (error instanceof z.ZodError) {
-        throw new Error(`Invalid arguments for prompt '${name}': ${error.message}`);
+        throw new Error(
+          `Invalid arguments for prompt '${name}': ${error.message}`
+        );
       }
       throw error;
     }
@@ -3132,7 +2497,9 @@ class McpResourcesManager {
     try {
       new ResourceTemplateParser(config.uriTemplate);
     } catch (error) {
-      throw new Error(`Invalid URI template '${config.uriTemplate}': ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Invalid URI template '${config.uriTemplate}': ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   /**
@@ -3237,6 +2604,97 @@ const _FlagManager = class _FlagManager {
 __flags = new WeakMap();
 _throwForDuplicateFlags = new WeakMap();
 let FlagManager = _FlagManager;
+function detectEntryPoint() {
+  try {
+    if (process.argv[1] && fs.existsSync(process.argv[1])) {
+      return process.argv[1];
+    }
+    if (typeof require !== "undefined" && require.main && require.main.filename) {
+      return require.main.filename;
+    }
+    return null;
+  } catch {
+    return null;
+  }
+}
+function getEntryPointFromImportMeta(importMetaUrl) {
+  if (importMetaUrl.startsWith("file://")) {
+    return decodeURIComponent(importMetaUrl.replace("file://", ""));
+  }
+  return importMetaUrl;
+}
+function normalizePath(path2) {
+  return path2.trim();
+}
+function resolveLogPath(logPath, fallbackEntryPoint) {
+  if (typeof logPath === "string") {
+    const normalizedPath2 = normalizePath(logPath);
+    if (path.isAbsolute(normalizedPath2)) {
+      return normalizedPath2;
+    }
+    if (normalizedPath2.startsWith("cwd:")) {
+      const relativePath = normalizedPath2.slice(4);
+      return path.resolve(process.cwd(), relativePath);
+    }
+    const entryPoint = detectEntryPoint() || fallbackEntryPoint;
+    if (entryPoint) {
+      return path.resolve(path.dirname(entryPoint), normalizedPath2);
+    }
+    console.warn(
+      `Warning: Could not detect entry point for log path resolution. Using process.cwd() as fallback. Path: ${normalizedPath2}`
+    );
+    return path.resolve(process.cwd(), normalizedPath2);
+  }
+  const { path: logFilePath, relativeTo = "entry", basePath } = logPath;
+  const normalizedPath = normalizePath(logFilePath);
+  switch (relativeTo) {
+    case "absolute":
+      if (basePath) {
+        return path.resolve(basePath, normalizedPath);
+      }
+      if (path.isAbsolute(normalizedPath)) {
+        return normalizedPath;
+      }
+      console.warn(
+        `Warning: relativeTo 'absolute' specified but no basePath provided and path is not absolute. Using process.cwd() as fallback. Path: ${normalizedPath}`
+      );
+      return path.resolve(process.cwd(), normalizedPath);
+    case "cwd":
+      return path.resolve(process.cwd(), normalizedPath);
+    case "entry":
+    default:
+      const entryPoint = detectEntryPoint() || fallbackEntryPoint;
+      if (entryPoint) {
+        return path.resolve(path.dirname(entryPoint), normalizedPath);
+      }
+      console.warn(
+        `Warning: Could not detect entry point for log path resolution. Using process.cwd() as fallback. Path: ${normalizedPath}`
+      );
+      return path.resolve(process.cwd(), normalizedPath);
+  }
+}
+function entryRelative(path2) {
+  return {
+    path: path2,
+    relativeTo: "entry"
+  };
+}
+function cwdRelative(path2) {
+  return {
+    path: path2,
+    relativeTo: "cwd"
+  };
+}
+function absolutePath(path2, basePath) {
+  return {
+    path: path2,
+    relativeTo: "absolute",
+    basePath
+  };
+}
+function legacyCwdPath(path2) {
+  return `cwd:${path2}`;
+}
 class ArgParserError extends Error {
   constructor(message, cmdChain = []) {
     super(message);
@@ -4634,15 +4092,14 @@ _handleBuildDxtFlag_fn = async function(processArgs, buildDxtIndex) {
 };
 _handleMcpServeFlag_fn = async function(processArgs, _mcpServeIndex) {
   var _a;
+  const transportOptions = __privateMethod(this, _ArgParserBase_instances, _parseMcpTransportOptions_fn).call(this, processArgs);
+  const mcpServerConfig = __privateMethod(this, _ArgParserBase_instances, _getMcpServerConfiguration_fn).call(this);
+  const effectiveLogPath = transportOptions.logPath || (mcpServerConfig == null ? void 0 : mcpServerConfig.logPath) || "./logs/mcp.log";
+  const resolvedLogPath = resolveLogPath(effectiveLogPath);
   let mcpLogger;
   try {
-    const mcpLoggerModule = await Function(
-      'return import("@alcyone-labs/simple-mcp-logger")'
-    )();
-    mcpLogger = mcpLoggerModule.createMcpLogger(
-      "MCP Serve",
-      "./logs/mcp.log"
-    );
+    const mcpLoggerModule = await import("@alcyone-labs/simple-mcp-logger");
+    mcpLogger = mcpLoggerModule.createMcpLogger("MCP Serve", resolvedLogPath);
     globalThis.console = mcpLogger;
   } catch {
     mcpLogger = {
@@ -4653,7 +4110,6 @@ _handleMcpServeFlag_fn = async function(processArgs, _mcpServeIndex) {
     mcpLogger.mcpError(
       "Starting --s-mcp-serve system flag handler - console hijacked for MCP safety"
     );
-    const mcpServerConfig = __privateMethod(this, _ArgParserBase_instances, _getMcpServerConfiguration_fn).call(this);
     if (!mcpServerConfig) {
       mcpLogger.mcpError(
         "No MCP server configuration found. Use withMcp() or addMcpSubCommand() to configure MCP server."
@@ -4667,13 +4123,16 @@ _handleMcpServeFlag_fn = async function(processArgs, _mcpServeIndex) {
     mcpLogger.mcpError(
       `Found MCP server configuration: ${((_a = mcpServerConfig.serverInfo) == null ? void 0 : _a.name) || "unnamed"}`
     );
-    const transportOptions = __privateMethod(this, _ArgParserBase_instances, _parseMcpTransportOptions_fn).call(this, processArgs);
+    mcpLogger.mcpError(`Using log path: ${resolvedLogPath}`);
     mcpLogger.mcpError(
       `Transport options: ${JSON.stringify(transportOptions)}`
     );
     try {
       mcpLogger.mcpError("Starting unified MCP server with all tools");
-      await __privateMethod(this, _ArgParserBase_instances, _startUnifiedMcpServer_fn).call(this, mcpServerConfig, transportOptions);
+      await __privateMethod(this, _ArgParserBase_instances, _startUnifiedMcpServer_fn).call(this, mcpServerConfig, {
+        ...transportOptions,
+        logPath: resolvedLogPath
+      });
       mcpLogger.mcpError("Successfully started unified MCP server");
     } catch (error) {
       mcpLogger.mcpError(
@@ -4742,18 +4201,34 @@ _startUnifiedMcpServer_fn = async function(mcpServerConfig, transportOptions) {
       await mcpParser.startMcpServerWithMultipleTransports(
         serverInfo,
         transportConfigs,
-        toolOptions
+        toolOptions,
+        transportOptions.logPath
       );
     } catch (error) {
       throw new Error(
         `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,
       defaultTransports,
-      toolOptions
+      toolOptions,
+      transportOptions.logPath
     );
   } else if (defaultTransport) {
     await mcpParser.startMcpServerWithTransport(
@@ -4765,20 +4240,16 @@ _startUnifiedMcpServer_fn = async function(mcpServerConfig, transportOptions) {
         path: defaultTransport.path,
         sessionIdGenerator: defaultTransport.sessionIdGenerator
       },
-      toolOptions
+      toolOptions,
+      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,
-      toolOptions
+      "stdio",
+      {},
+      toolOptions,
+      transportOptions.logPath
     );
   }
 };
@@ -4845,6 +4316,12 @@ _parseMcpTransportOptions_fn = function(processArgs) {
           i++;
         }
         break;
+      case "--s-mcp-log-path":
+        if (nextArg && !nextArg.startsWith("-")) {
+          options.logPath = nextArg;
+          i++;
+        }
+        break;
       // Backward compatibility: support old flags but with deprecation warning
       case "--transport":
       case "--port":
@@ -6130,11 +5607,14 @@ Migration guide: https://github.com/alcyone-labs/arg-parser/blob/main/docs/MCP-M
    * @param toolOptions Optional MCP tool generation options
    * @returns Configured MCP server instance
    */
-  async createMcpServer(serverInfo, toolOptions) {
-    var _a;
-    const logger2 = createMcpLogger("MCP Server Creation", "./logs/mcp.log");
+  async createMcpServer(serverInfo, toolOptions, logPath) {
+    var _a, _b;
+    const resolvedLogPath = resolveLogPath(
+      logPath || ((_a = this._mcpServerConfig) == null ? void 0 : _a.logPath) || "./logs/mcp.log"
+    );
+    const logger2 = createMcpLogger("MCP Server Creation", resolvedLogPath);
     try {
-      const effectiveServerInfo = serverInfo || ((_a = this._mcpServerConfig) == null ? void 0 : _a.serverInfo);
+      const effectiveServerInfo = serverInfo || ((_b = this._mcpServerConfig) == null ? void 0 : _b.serverInfo);
       if (!effectiveServerInfo) {
         throw new Error(
           "No MCP server configuration found. Use withMcp() to configure server info or provide serverInfo parameter."
@@ -6315,11 +5795,11 @@ Migration guide: https://github.com/alcyone-labs/arg-parser/blob/main/docs/MCP-M
    * @param toolOptions Optional MCP tool generation options
    * @returns Promise that resolves when all servers are started
    */
-  async startMcpServerWithMultipleTransports(serverInfo, transports, toolOptions) {
-    const server = await this.createMcpServer(serverInfo, toolOptions);
+  async startMcpServerWithMultipleTransports(serverInfo, transports, toolOptions, logPath) {
+    const server = await this.createMcpServer(serverInfo, toolOptions, logPath);
     const startPromises = [];
     for (const transportConfig of transports) {
-      const promise = __privateMethod(this, _ArgParser_instances, _startSingleTransport_fn).call(this, server, serverInfo, transportConfig);
+      const promise = __privateMethod(this, _ArgParser_instances, _startSingleTransport_fn).call(this, server, serverInfo, transportConfig, logPath);
       startPromises.push(promise);
     }
     await Promise.all(startPromises);
@@ -6332,12 +5812,12 @@ Migration guide: https://github.com/alcyone-labs/arg-parser/blob/main/docs/MCP-M
    * @param toolOptions Optional MCP tool generation options
    * @returns Promise that resolves when server is connected
    */
-  async startMcpServerWithTransport(serverInfo, transportType, transportOptions = {}, toolOptions) {
-    const server = await this.createMcpServer(serverInfo, toolOptions);
+  async startMcpServerWithTransport(serverInfo, transportType, transportOptions = {}, toolOptions, logPath) {
+    const server = await this.createMcpServer(serverInfo, toolOptions, logPath);
     await __privateMethod(this, _ArgParser_instances, _startSingleTransport_fn).call(this, server, serverInfo, {
       type: transportType,
       ...transportOptions
-    });
+    }, logPath);
   }
   async parse(processArgs, options) {
     let result = await ArgParserBase.prototype.parse.call(
@@ -6599,8 +6079,9 @@ registerToolAsSubCommand_fn = function(toolConfig) {
     handler: toolConfig.handler
   });
 };
-_startSingleTransport_fn = async function(server, serverInfo, transportConfig) {
-  const logger2 = createMcpLogger("MCP Transport", "./logs/mcp.log");
+_startSingleTransport_fn = async function(server, serverInfo, transportConfig, logPath) {
+  const resolvedLogPath = resolveLogPath(logPath || "./logs/mcp.log");
+  const logger2 = createMcpLogger("MCP Transport", resolvedLogPath);
   try {
     logger2.mcpError(
       `Starting ${transportConfig.type} transport for server: ${serverInfo.name}`
@@ -6776,7 +6257,9 @@ class TomlConfigPlugin extends ConfigPlugin {
       }
       return parsed;
     } catch (error) {
-      throw new Error(`Failed to parse TOML: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to parse TOML: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   generate(_config, flags, parsedArgs) {
@@ -6816,7 +6299,9 @@ class TomlConfigPlugin extends ConfigPlugin {
       const tomlContent = this.tomlModule.stringify(configWithValues);
       return lines.join("\n") + "\n" + tomlContent;
     } catch (error) {
-      throw new Error(`Failed to generate TOML: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to generate TOML: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   /**
@@ -6852,7 +6337,10 @@ function createTomlPlugin() {
   try {
     return new TomlConfigPlugin();
   } catch (error) {
-    console.warn("TOML plugin not available:", error instanceof Error ? error.message : String(error));
+    console.warn(
+      "TOML plugin not available:",
+      error instanceof Error ? error.message : String(error)
+    );
     return null;
   }
 }
@@ -6868,7 +6356,10 @@ async function createTomlPluginAsync() {
     const tomlModule = await Promise.resolve().then(() => index$1);
     return new TomlConfigPlugin(tomlModule);
   } catch (error) {
-    console.warn("TOML plugin not available:", error instanceof Error ? error.message : String(error));
+    console.warn(
+      "TOML plugin not available:",
+      error instanceof Error ? error.message : String(error)
+    );
     return null;
   }
 }
@@ -6914,7 +6405,9 @@ class YamlConfigPlugin extends ConfigPlugin {
       }
       return parsed;
     } catch (error) {
-      throw new Error(`Failed to parse YAML: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to parse YAML: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   generate(_config, flags, parsedArgs) {
@@ -6948,7 +6441,9 @@ class YamlConfigPlugin extends ConfigPlugin {
       });
       return lines.join("\n") + "\n" + yamlContent;
     } catch (error) {
-      throw new Error(`Failed to generate YAML: ${error instanceof Error ? error.message : String(error)}`);
+      throw new Error(
+        `Failed to generate YAML: ${error instanceof Error ? error.message : String(error)}`
+      );
     }
   }
   /**
@@ -6978,7 +6473,10 @@ function createYamlPlugin() {
   try {
     return new YamlConfigPlugin();
   } catch (error) {
-    console.warn("YAML plugin not available:", error instanceof Error ? error.message : String(error));
+    console.warn(
+      "YAML plugin not available:",
+      error instanceof Error ? error.message : String(error)
+    );
     return null;
   }
 }
@@ -6994,7 +6492,10 @@ async function createYamlPluginAsync() {
     const yamlModule = await import("js-yaml");
     return new YamlConfigPlugin(yamlModule);
   } catch (error) {
-    console.warn("YAML plugin not available:", error instanceof Error ? error.message : String(error));
+    console.warn(
+      "YAML plugin not available:",
+      error instanceof Error ? error.message : String(error)
+    );
     return null;
   }
 }
@@ -7023,7 +6524,9 @@ class ArgParserFuzzyTester {
     const results = [];
     if (this.options.verbose) {
       console.log(`Discovered ${commandPaths.length} command paths:`);
-      commandPaths.forEach((path2) => console.log(`  ${path2.join(" ") || "(root)"}`));
+      commandPaths.forEach(
+        (path2) => console.log(`  ${path2.join(" ") || "(root)"}`)
+      );
     }
     for (const commandPath of commandPaths) {
       const pathResults = await this.testCommandPath(commandPath);
@@ -7049,7 +6552,12 @@ class ArgParserFuzzyTester {
     for (const [subCommandName, subCommand] of subCommands) {
       const newPath = [...currentPath, subCommandName];
       allPaths.push(newPath);
-      this.discoverSubCommandPaths(subCommand.parser, newPath, allPaths, depth + 1);
+      this.discoverSubCommandPaths(
+        subCommand.parser,
+        newPath,
+        allPaths,
+        depth + 1
+      );
     }
   }
   /**
@@ -8266,6 +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);
@@ -8347,6 +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");
@@ -8546,10 +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"
@@ -24941,6 +24473,7 @@ export {
   simpleChalk as SimpleChalk,
   TomlConfigPlugin,
   YamlConfigPlugin,
+  absolutePath,
   convertFlagToJsonSchemaProperty,
   convertFlagsToJsonSchema,
   convertFlagsToZodSchema,
@@ -24954,14 +24487,20 @@ export {
   createTomlPluginAsync,
   createYamlPlugin,
   createYamlPluginAsync,
+  cwdRelative,
+  detectEntryPoint,
   enableConfigPlugins,
   enableOptionalConfigPlugins,
   enableOptionalConfigPluginsAsync,
+  entryRelative,
   extractSimplifiedResponse,
   generateMcpToolsFromArgParser,
+  getEntryPointFromImportMeta,
   getJsonSchemaTypeFromFlag,
   globalConfigPluginRegistry,
+  legacyCwdPath,
   logger,
+  resolveLogPath,
   zodFlagSchema
 };
 //# sourceMappingURL=index.mjs.map