Clean also wipes out the www directory, which was causing the strange errors that were happening when building

bin/templates/cordova/Api.js

@@ -18,6 +18,7 @@
 */
 
 var path = require('path');
+var nopt = require('nopt');
 var Q = require('q');
 
 var AndroidProject = require('./lib/AndroidProject');
@@ -29,6 +30,7 @@ var selfEvents = require('cordova-common').events;
 
 var PLATFORM = 'android';
 
+
 function setupEvents(externalEventEmitter) {
     if (externalEventEmitter) {
         // This will make the platform internal events visible outside
@@ -219,7 +221,17 @@ Api.prototype.addPlugin = function (plugin, installOptions) {
             //CB-11964: Do a clean when installing the plugin code to get around
             //the Gradle bug introduced by the Android Gradle Plugin Version 2.2
             //TODO: Delete when the next version of Android Gradle plugin comes out
-            return self.clean();
+
+           // Since clean doesn't just clean the build, it also wipes out www, we need
+           // to pass additional options.
+
+           // Do some basic argument parsing
+            var opts = {};
+
+            // Skip cleaning prepared files when not invoking via cordova CLI.
+            opts.noPrepare = true;
+
+            return self.clean(opts);
         })
        .then(function () {
             return PluginManager.get(self.platform, self.locations, project)
@@ -353,7 +365,8 @@ Api.prototype.run = function(runOptions) {
 };
 
 /**
- * Cleans out the build artifacts from platform's directory.
+ * Cleans out the build artifacts from platform's directory, and also
+ * cleans out the platform www directory if called without options specified.
  *
  * @return  {Promise}  Return a promise either fulfilled, or rejected with
  *   CordovaError.