seems to all work

bin/letsencrypt.js

@@ -19,7 +19,7 @@ cli.parse({
 , 'domain-key-path': [ false, " Path to privkey.pem to use for domain (default: generate new)", 'string' ]
 , 'config-dir': [ false, " Configuration directory.", 'string', '~/letsencrypt/etc/' ]
 , server: [ false, " ACME Directory Resource URI.", 'string', 'https://acme-v01.api.letsencrypt.org/directory)' ]
-, standalone: [ false, " Obtain certs using a \"standalone\" webserver.", 'boolean', true ]
+, standalone: [ false, " Obtain certs using a \"standalone\" webserver.", 'boolean', false ]
 //, manual: [ false, " Provide laborious manual instructions for obtaining a cert (default: false)", 'boolean', false ]
 , webroot: [ false, " Obtain certs by placing files in a webroot directory.", 'boolean', false ]
 , 'webroot-path': [ false, " public_html / webroot path.", 'string' ]
@@ -80,17 +80,19 @@ cli.main(function(_, options) {
     var LE = require('letsencrypt');
     var handlers;
 
-    if (args.standalone) {
+    if (args.webrootPath) {
+      handlers = require('../lib/webroot').create(args);
+    }
+    else /*if (args.standalone)*/ {
       handlers = require('../lib/standalone').create();
       handlers.startServers(args.http01Ports || [80], args.tlsSni01Port || [443, 5001]);
     }
-    else if (args.webrootPath) {
-      handlers = require('../lib/webroot').create(args);
-    }
 
-    LE.create({}, handlers).register(args, function (err, results) {
+    // let LE know that we're handling standalone / webroot here
+    LE.create({ manual: true }, handlers).register(args, function (err, results) {
       if (err) {
-        console.error(err.stack);
+        console.error('[Error]: letsencrypt');
+        console.error(err);
         return;
       }
 

lib/standalone.js

@@ -1,7 +1,7 @@
 'use strict';
 
-var handlers = module.exports.create = function () {
-  return {
+module.exports.create = function () {
+  var handlers =  {
     //
     // set,get,remove challenges
     //
@@ -66,4 +66,6 @@ var handlers = module.exports.create = function () {
       handlers._servers = [];
     }
   };
+
+  return handlers;
 };

lib/webroot.js

@@ -1,11 +1,11 @@
 'use strict';
 
-var handlers = module.exports.create = function (defaults) {
+module.exports.create = function (defaults) {
   var fs = require('fs');
   var path = require('path');
   var mkdirp = require('mkdirp');
 
-  return {
+  var handlers = {
     //
     // set,get,remove challenges
     //
@@ -48,4 +48,6 @@ var handlers = module.exports.create = function (defaults) {
       });
     }
   };
+
+  return handlers;
 };