Create a copy of each app's shim bundle in the app's app_data_path.

chrome/browser/web_applications/web_app_mac.mm

 // Copyright (c) 2012 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
 #import "chrome/browser/web_applications/web_app_mac.h"
 
 #import <Carbon/Carbon.h>
 #import <Cocoa/Cocoa.h>
 
 #include "base/command_line.h"
@@ skipping 177 matching lines @@
 }
 
 bool WebAppShortcutCreator::CreateShortcut() {
   base::FilePath app_path = GetShortcutPath();
   base::FilePath app_name = app_path.BaseName();
   base::FilePath dst_path = app_path.DirName();
   if (app_path.empty() || !file_util::DirectoryExists(dst_path.DirName())) {
     LOG(ERROR) << "Couldn't find an Applications directory to copy app to.";
     return false;
   }
+  if (!file_util::CreateDirectory(user_data_dir_)) {
+    LOG(ERROR) << "Creating user_data_dir " << user_data_dir_.value()
+               << " failed.";
+    return false;
+  }
   if (!file_util::CreateDirectory(dst_path)) {
     LOG(ERROR) << "Creating directory " << dst_path.value() << " failed.";
     return false;
   }
 
   base::ScopedTempDir scoped_temp_dir;
   if (!scoped_temp_dir.CreateUniqueTempDir())
     return false;
   base::FilePath staging_path = scoped_temp_dir.path().Append(app_name);
 
   // Update the app's plist and icon in a temp directory. This works around
   // a Finder bug where the app's icon doesn't properly update.
   if (!file_util::CopyDirectory(GetAppLoaderPath(), staging_path, true)) {
     LOG(ERROR) << "Copying app to staging path: " << staging_path.value()
-               << " failed";
+               << " failed.";
     return false;
   }
 
   if (!UpdatePlist(staging_path))
     return false;
 
   if (!UpdateDisplayName(staging_path))
     return false;
 
   if (!UpdateIcon(staging_path))
     return false;
 
-  if (!file_util::CopyDirectory(staging_path, dst_path, true)) {
-    LOG(ERROR) << "Copying app to dst path: " << dst_path.value() << " failed";
+  // Put one copy in the app's user_data_dir so we can still run it if the user
+  // deletes the one in the applications folder.
+  if (!file_util::CopyDirectory(staging_path, user_data_dir_, true)) {
+    NOTREACHED();
     return false;
   }
+  base::mac::RemoveQuarantineAttribute(user_data_dir_.Append(app_name));
+
+  if (!file_util::CopyDirectory(staging_path, dst_path, true))
+    return false;
 
   base::mac::RemoveQuarantineAttribute(app_path);
+
   RevealGeneratedBundleInFinder(app_path);
 
   return true;
 }
 
 base::FilePath WebAppShortcutCreator::GetAppLoaderPath() const {
   return base::mac::PathForFrameworkBundleResource(
       base::mac::NSToCFCast(@"app_mode_loader.app"));
 }
 
@@ skipping 134 matching lines @@
     const base::FilePath& generated_bundle) const {
   [[NSWorkspace sharedWorkspace]
                     selectFile:base::mac::FilePathToNSString(generated_bundle)
       inFileViewerRootedAtPath:nil];
 }
 
 void LaunchShimOnFileThread(
       const ShellIntegration::ShortcutInfo& shortcut_info) {
   DCHECK(content::BrowserThread::CurrentlyOn(content::BrowserThread::FILE));
   base::FilePath shim_path = web_app::GetAppInstallPath(shortcut_info);
-  if (shim_path.empty())
-    return;
+
+  if (!file_util::PathExists(shim_path)) {

[tapted, 2013/06/12 08:37:56]

This should be 

if (shim_path.empty() || !file_util::PathExists(shim_path))

[jackhou1, 2013/06/12 09:05:18]

Done.

+    // The user may have deleted the copy in the Applications folder, use the
+    // one in the web app's user_data_dir.
+    base::FilePath shortcut_data_dir = GetWebAppDataDirectory(
+        shortcut_info.profile_path, shortcut_info.extension_id, GURL());
+    shim_path = shortcut_data_dir.Append(shim_path.BaseName());
+  }
 
   CommandLine command_line(CommandLine::NO_PROGRAM);
   command_line.AppendSwitch(app_mode::kNoLaunchApp);
   base::mac::OpenApplicationWithPath(shim_path, command_line, NULL);
 }
 
 }  // namespace
 
 namespace web_app {
 
@@ skipping 59 matching lines @@
     const base::FilePath& web_app_path,
     const string16& old_app_title,
     const ShellIntegration::ShortcutInfo& shortcut_info) {
   // TODO(benwells): Implement this when shortcuts / weblings are enabled on
   // mac.
 }
 
 }  // namespace internals
 
 }  // namespace web_app