Open the notification URL (not the web app start_url) when deep-linking into standalone mode.

chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java

Index: chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java
diff --git a/chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java b/chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java
index c8f7a54f2defa9c9d5d7dc0d1a89863a3f408e7f..0f4bcad6e7ff95d653247725292ce73348270cb3 100644
--- a/chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java
+++ b/chrome/android/java/src/org/chromium/chrome/browser/ChromeServiceTabLauncher.java
@@ -96,6 +96,9 @@ public class ChromeServiceTabLauncher extends ServiceTabLauncher {
 
                         @Override
                         protected final void onPostExecute(Intent intent) {
+                            // Replace the web app URL with the URL from the notification. This is
+                            // within the webapp's scope, so it is valid.
+                            intent.putExtra(ShortcutHelper.EXTRA_URL, url);
                             intent.putExtra(ShortcutHelper.EXTRA_SOURCE,
                                     ShortcutSource.NOTIFICATION);
                             tabDelegate.createNewStandaloneFrame(intent);