force plugins to be ran at all times - fixes #1450

src/babel/transformation/file/plugin-manager.js

@@ -57,6 +57,9 @@ export default class PluginManager {
     if (!plugin.buildPass || plugin.constructor.name !== "Transformer") {
       throw new TypeError(messages.get("pluginNotTransformer", name));
     }
+
+    // register as a plugin
+    plugin.metadata.plugin = true;
   }
 
   add(name) {

src/babel/transformation/transformer-pipeline.js

@@ -47,6 +47,8 @@ export default class TransformerPipeline {
   }
 
   canTransform(transformer, fileOpts) {
+    if (transformer.metadata.plugin) return true;
+
     for (var filter of (this.filters: Array)) {
       var result = filter(transformer, fileOpts);
       if (result != null) return result;