Alternatively, it looks like the nested arrays could be avoided altogether with the following change in has.js.  This is probably a better solution.
```javascript
 					module = getAmdModule(resolvedId, referenceModule);
 				if(module){
 					referenceModule.text = referenceModule.text.replace(regex, resolvedId);
-					return [module];
+					return lang.isArray(module) ? module : [module];
 				}else{
 					bc.log("dojoHasMissingMid", ["plugin resource id", id, "resolved plugin resource id", moduleInfo.mid, "reference module id", referenceModule && referenceModule.mid]);
 					return getHasPluginDependency();
```