diff --git a/bin/6to5/index.js b/bin/6to5/index.js
index da2137456a..0cd6382a1c 100755
--- a/bin/6to5/index.js
+++ b/bin/6to5/index.js
@@ -22,7 +22,6 @@ commander.option("--loose [list]", "List of transformers to enable their loose m
 commander.option("-o, --out-file [out]", "Compile all input files into a single file");
 commander.option("-d, --out-dir [out]", "Compile an input directory of modules into an output directory");
 commander.option("-c, --remove-comments", "Remove comments from the compiled code", false);
-commander.option("-a, --amd-module-ids", "Insert module id in AMD modules", false); // todo: remove in 3.0.0
 commander.option("-m, --module-ids", "Insert module id in modules", false);
 commander.option("-R, --react-compat", "Makes the react transformer produce pre-v0.12 code");
 commander.option("-E, --include-regenerator", "Include the regenerator runtime if necessary", false);
@@ -100,7 +99,7 @@ exports.opts = {
   experimental:           commander.experimental,
   reactCompat:            commander.reactCompat,
   playground:             commander.playground,
-  moduleIds:              commander.amdModuleIds || commander.moduleIds,
+  moduleIds:              commander.moduleIds,
   blacklist:              commander.blacklist,
   whitelist:              commander.whitelist,
   sourceMap:              commander.sourceMaps || commander.sourceMapsInline,
diff --git a/lib/6to5/file.js b/lib/6to5/file.js
index b22bf8220e..5c953ba7f2 100644
--- a/lib/6to5/file.js
+++ b/lib/6to5/file.js
@@ -48,9 +48,10 @@ File.helpers = [
 
 File.validOptions = [
   "filename",
-  "fileNameRelative",
+  "filenameRelative",
   "blacklist",
   "whitelist",
+  "loose",
   "optional",
   "modules",
   "sourceMap",
@@ -85,7 +86,7 @@ File.normaliseOptions = function (opts) {
     reactCompat:            false,
     playground:             false,
     whitespace:             true,
-    moduleIds:              opts.amdModuleIds || false,
+    moduleIds:              false,
     blacklist:              [],
     whitelist:              [],
     sourceMap:              false,
diff --git a/test/_transformation-helper.js b/test/_transformation-helper.js
index c036440f9e..77ae528105 100644
--- a/test/_transformation-helper.js
+++ b/test/_transformation-helper.js
@@ -49,8 +49,11 @@ var run = function (task, done) {
   var execCode = exec.code;
   var result;
 
+  var noCheckAst = opts.noCheckAst;
+  delete opts.noCheckAst;
+
   var checkAst = function (result) {
-    if (opts.noCheckAst) return;
+    if (noCheckAst) return;
 
     var errors = esvalid.errors(result.ast.program);
     if (errors.length) {
diff --git a/test/fixtures/transformation/es6-modules-amd/module-name/options.json b/test/fixtures/transformation/es6-modules-amd/module-name/options.json
index a2868455b4..be49a87d0b 100644
--- a/test/fixtures/transformation/es6-modules-amd/module-name/options.json
+++ b/test/fixtures/transformation/es6-modules-amd/module-name/options.json
@@ -1,3 +1,3 @@
 {
-  "amdModuleIds": true
+  "moduleIds": true
 }
diff --git a/test/fixtures/transformation/es6-modules-umd/module-name/options.json b/test/fixtures/transformation/es6-modules-umd/module-name/options.json
index a2868455b4..be49a87d0b 100644
--- a/test/fixtures/transformation/es6-modules-umd/module-name/options.json
+++ b/test/fixtures/transformation/es6-modules-umd/module-name/options.json
@@ -1,3 +1,3 @@
 {
-  "amdModuleIds": true
+  "moduleIds": true
 }