diff --git a/tools/broccoli/broccoli-tree-stabilizer.ts b/tools/broccoli/broccoli-tree-stabilizer.ts
new file mode 100644
index 0000000000..9a1bf97a4f
--- /dev/null
+++ b/tools/broccoli/broccoli-tree-stabilizer.ts
@@ -0,0 +1,45 @@
+/// <reference path="broccoli.d.ts" />
+/// <reference path="../typings/node/node.d.ts" />
+
+import fs = require('fs');
+let symlinkOrCopy = require('symlink-or-copy');
+
+
+/**
+ * Stabilizes the inputPath for the following plugins in the build tree.
+ *
+ * All broccoli plugins that inherit from `broccoli-writer` or `broccoli-filter` change their
+ * outputPath during each rebuild.
+ *
+ * This means that all following plugins in the build tree can't rely on their inputPath being
+ * immutable. This results in breakage of any plugin that is not expecting such behavior.
+ *
+ * For example all `DiffingBroccoliPlugin`s expect their inputPath to be stable.
+ *
+ * By inserting this plugin into the tree after any misbehaving plugin, we can stabilize the
+ * inputPath for the following plugin in the tree and correct the surprising behavior.
+ */
+class TreeStabilizer implements BroccoliTree {
+  inputPath: string;
+  outputPath: string;
+
+
+  constructor(public inputTree: BroccoliTree) {}
+
+
+  rebuild() {
+    fs.rmdirSync(this.outputPath);
+
+    // TODO: investigate if we can use rename the directory instead to improve performance on
+    // Windows
+    symlinkOrCopy.sync(this.inputPath, this.outputPath);
+  }
+
+
+  cleanup() {}
+}
+
+
+export default function stabilizeTree(inputTree) {
+  return new TreeStabilizer(inputTree);
+}
diff --git a/tools/broccoli/diffing-broccoli-plugin.ts b/tools/broccoli/diffing-broccoli-plugin.ts
index ae133996a2..dc03289591 100644
--- a/tools/broccoli/diffing-broccoli-plugin.ts
+++ b/tools/broccoli/diffing-broccoli-plugin.ts
@@ -6,6 +6,7 @@ import fs = require('fs');
 import fse = require('fs-extra');
 import path = require('path');
 import {TreeDiffer, DiffResult} from './tree-differ';
+import stabilizeTree from './broccoli-tree-stabilizer';
 let symlinkOrCopy = require('symlink-or-copy');
 
 
@@ -51,9 +52,9 @@ class DiffingPluginWrapper implements BroccoliTree {
 
   constructor(private pluginClass, private wrappedPluginArguments) {
     if (Array.isArray(wrappedPluginArguments[0])) {
-      this.inputTrees = wrappedPluginArguments[0];
+      this.inputTrees = this.stabilizeTrees(wrappedPluginArguments[0]);
     } else {
-      this.inputTree = wrappedPluginArguments[0];
+      this.inputTree = this.stabilizeTree(wrappedPluginArguments[0]);
     }
 
     this.description = this.pluginClass.name;
@@ -82,6 +83,13 @@ class DiffingPluginWrapper implements BroccoliTree {
   }
 
 
+  cleanup() {
+    if (this.wrappedPlugin.cleanup) {
+      this.wrappedPlugin.cleanup();
+    }
+  }
+
+
   private relinkOutputAndCachePaths() {
     // just symlink the cache and output tree
     fs.rmdirSync(this.outputPath);
@@ -101,9 +109,15 @@ class DiffingPluginWrapper implements BroccoliTree {
   }
 
 
-  cleanup() {
-    if (this.wrappedPlugin.cleanup) {
-      this.wrappedPlugin.cleanup();
-    }
+  private stabilizeTrees(trees: BroccoliTree[]) {
+    return trees.map((tree) => this.stabilizeTree(tree));
+  }
+
+
+  private stabilizeTree(tree: BroccoliTree) {
+    // Ignore all DiffingPlugins as they are already stable, for others we don't know for sure
+    // so we need to stabilize them.
+    // Since it's not safe to use instanceof operator in node, we are checking the constructor.name.
+    return (tree.constructor['name'] === 'DiffingPluginWrapper') ? tree : stabilizeTree(tree);
   }
 }
diff --git a/tools/broccoli/trees/browser_tree.ts b/tools/broccoli/trees/browser_tree.ts
index c16eccdf88..3df98400cf 100644
--- a/tools/broccoli/trees/browser_tree.ts
+++ b/tools/broccoli/trees/browser_tree.ts
@@ -56,11 +56,6 @@ module.exports = function makeBrowserTree(options, destinationPath) {
 
   var es6Tree = mergeTrees([traceurTree, typescriptTree]);
 
-  // TODO(iminar): tree differ seems to have issues with trees created by mergeTrees, investigate!
-  //   ENOENT error is thrown while doing fs.readdirSync on inputRoot
-  //   in the meantime, we just do noop mv to create a new tree
-  es6Tree = stew.mv(es6Tree, '');
-
   // Call Traceur again to lower the ES6 build tree to ES5
   var es5Tree = transpileWithTraceur(es6Tree, {
     destExtension: '.js',
@@ -152,10 +147,5 @@ module.exports = function makeBrowserTree(options, destinationPath) {
 
   var mergedTree = mergeTrees([stew.mv(es6Tree, '/es6'), stew.mv(es5Tree, '/es5')]);
 
-  // TODO(iminar): tree differ seems to have issues with trees created by mergeTrees, investigate!
-  //   ENOENT error is thrown while doing fs.readdirSync on inputRoot
-  //   in the meantime, we just do noop mv to create a new tree
-  mergedTree = stew.mv(mergedTree, '');
-
   return destCopy(mergedTree, destinationPath);
 };
diff --git a/tools/broccoli/trees/dart_tree.ts b/tools/broccoli/trees/dart_tree.ts
index 82c965e278..d95f16d030 100644
--- a/tools/broccoli/trees/dart_tree.ts
+++ b/tools/broccoli/trees/dart_tree.ts
@@ -144,10 +144,5 @@ module.exports = function makeDartTree(destinationPath) {
 
   var dartTree = mergeTrees([sourceTree, getTemplatedPubspecsTree(), getDocsTree()]);
 
-  // TODO(iminar): tree differ seems to have issues with trees created by mergeTrees, investigate!
-  //   ENOENT error is thrown while doing fs.readdirSync on inputRoot
-  //   in the meantime, we just do noop mv to create a new tree
-  dartTree = stew.mv(dartTree, '');
-
   return destCopy(dartTree, destinationPath);
 };
diff --git a/tools/broccoli/trees/node_tree.ts b/tools/broccoli/trees/node_tree.ts
index 539be352b7..8e59acfe18 100644
--- a/tools/broccoli/trees/node_tree.ts
+++ b/tools/broccoli/trees/node_tree.ts
@@ -96,11 +96,6 @@ module.exports = function makeNodeTree(destinationPath) {
     }
   });
 
-  // TODO(iminar): tree differ seems to have issues with trees created by mergeTrees, investigate!
-  //   ENOENT error is thrown while doing fs.readdirSync on inputRoot
-  //   in the meantime, we just do noop mv to create a new tree
-  traceurCompatibleTsModulesTree = stew.mv(traceurCompatibleTsModulesTree, '');
-
   var typescriptTree = compileWithTypescript(traceurCompatibleTsModulesTree, {
     allowNonTsExtensions: false,
     emitDecoratorMetadata: true,
@@ -131,12 +126,5 @@ module.exports = function makeNodeTree(destinationPath) {
     }]
   });
 
-
-
-  // TODO(iminar): tree differ seems to have issues with trees created by mergeTrees, investigate!
-  //   ENOENT error is thrown while doing fs.readdirSync on inputRoot
-  //   in the meantime, we just do noop mv to create a new tree
-  nodeTree = stew.mv(nodeTree, '');
-
   return destCopy(nodeTree, destinationPath);
 };