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

chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java

Index: chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java
diff --git a/chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java b/chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java
index c25ccaebbc11b28233f726ba673aa941fe847384..0b7ed276effc4fbe17defa62b5994fb3f5d858ef 100644
--- a/chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java
+++ b/chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappLauncherActivity.java
@@ -17,6 +17,7 @@ import org.chromium.base.ContextUtils;
 import org.chromium.base.Log;
 import org.chromium.chrome.browser.IntentHandler;
 import org.chromium.chrome.browser.ShortcutHelper;
+import org.chromium.chrome.browser.ShortcutSource;
 import org.chromium.chrome.browser.document.ChromeLauncherActivity;
 import org.chromium.chrome.browser.metrics.LaunchMetrics;
 import org.chromium.chrome.browser.tab.Tab;
@@ -87,6 +88,17 @@ public class WebappLauncherActivity extends Activity {
                 // Activity.
                 launchIntent.setAction(Intent.ACTION_VIEW);
                 launchIntent.setData(Uri.parse(WebappActivity.WEBAPP_SCHEME + "://" + webappId));
+
+                // If this is launching from a notification, we want to ensure that the URL being
+                // launched is the URL in the intent. If a paused WebappActivity exists for this id,
+                // then by default it will be focused and we have no way of sending the desired URL
+                // to it (the intent is swallowed). As a workaround, set the CLEAR_TOP flag to
+                // ensure that the existing Activity is cleared and relaunched with this intent.
+                // TODO(dominickn): ideally, we want be able to route an intent to
+                // WebappActivity.onNewIntent instead of restarting the Activity.
+                if (webappSource == ShortcutSource.NOTIFICATION) {
+                    launchIntent.setFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP);
+                }
             } else {
                 Log.e(TAG, "Shortcut (%s) opened in Chrome.", webappUrl);