diff --git a/package.json b/package.json
index 396ae9d6..24f782ab 100644
--- a/package.json
+++ b/package.json
@@ -13,6 +13,7 @@
     "jsonlint": "^1.6.3",
     "less": "^3.8.1",
     "lz-string-unsafe": "^1.4.4-fork-1",
+    "rimraf": "^2.6.2",
     "semver-bundle": "^0.1.1",
     "stylelint-bundle": "^8.0.0",
     "stylus-lang-bundle": "^0.54.5",
@@ -23,7 +24,7 @@
     "update": "npm run update-node && npm run update-main",
     "update-quick": "updates -u && npm update && npm run update-main",
     "update-main": "npm run update-versions && npm run update-codemirror",
-    "update-node": "updates -u && rm -rf node_modules && npm install",
+    "update-node": "updates -u && node tools/remove-modules.js && npm install",
     "update-codemirror": "node tools/update-libraries.js && node tools/update-codemirror-themes.js",
     "update-versions": "node tools/update-versions",
     "zip": "npm run update-versions && node tools/zip.js"
diff --git a/tools/remove-modules.js b/tools/remove-modules.js
new file mode 100644
index 00000000..c3b166ac
--- /dev/null
+++ b/tools/remove-modules.js
@@ -0,0 +1,8 @@
+#!/usr/bin/env node
+'use strict';
+
+const fs = require('fs');
+const rimraf = require('rimraf');
+
+// See https://github.com/isaacs/rimraf/issues/102#issuecomment-412310309
+rimraf('node_modules/!(rimraf|.bin)', fs, () => {});