Apps that don't appear on the NTP shouldn't contribute to NTP page overflow.

chrome/browser/extensions/extension_sorting.cc

 // 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.
 
 #include "chrome/browser/extensions/extension_sorting.h"
 
 #include <algorithm>
 #include <vector>
 
 #include "base/prefs/pref_service.h"
@@ skipping 346 matching lines @@
 syncer::StringOrdinal ExtensionSorting::GetNaturalAppPageOrdinal() const {
   const DictionaryValue* extensions = pref_service_->GetDictionary(
           ExtensionPrefs::kExtensionsPref);
   CHECK(extensions);
 
   if (ntp_ordinal_map_.empty())
     return syncer::StringOrdinal::CreateInitialOrdinal();
 
   for (PageOrdinalMap::const_iterator it = ntp_ordinal_map_.begin();
        it != ntp_ordinal_map_.end(); ++it) {
-    if (it->second.size() < kNaturalAppPageSize)
+    if (CountItemsVisibleOnNtp(it->second) < kNaturalAppPageSize)
       return it->first;
   }
 
   // Add a new page as all existing pages are full.
   syncer::StringOrdinal last_element = ntp_ordinal_map_.rbegin()->first;
   return last_element.CreateAfter();
 }
 
 syncer::StringOrdinal ExtensionSorting::GetPageOrdinal(
     const std::string& extension_id) const {
@@ skipping 60 matching lines @@
   if (page_index < ntp_ordinal_map_.size()) {
     PageOrdinalMap::const_iterator it = ntp_ordinal_map_.begin();
     std::advance(it, page_index);
     return it->first;
   }
 
   CreateOrdinalsIfNecessary(page_index + 1);
   return ntp_ordinal_map_.rbegin()->first;
 }
 
+void ExtensionSorting::MarkExtensionAsHidden(const std::string& extension_id) {
+  ntp_hidden_extensions_.insert(extension_id);
+}
+
 syncer::StringOrdinal ExtensionSorting::GetMinOrMaxAppLaunchOrdinalsOnPage(
     const syncer::StringOrdinal& target_page_ordinal,
     AppLaunchOrdinalReturn return_type) const {
   CHECK(target_page_ordinal.IsValid());
 
   syncer::StringOrdinal return_value;
 
   PageOrdinalMap::const_iterator page =
       ntp_ordinal_map_.find(target_page_ordinal);
   if (page != ntp_ordinal_map_.end()) {
@@ skipping 145 matching lines @@
     ++app_it;
 
   // If there is no next after the collision, returns the next ordinal.
   if (app_it == page.end())
     return app_launch_ordinal.CreateAfter();
 
   // Otherwise, returns the ordinal between the collision and the next ordinal.
   return app_launch_ordinal.CreateBetween(app_it->first);
 }
 
+size_t ExtensionSorting::CountItemsVisibleOnNtp(
+    const AppLaunchOrdinalMap& m) const {
+  size_t result = 0;
+  for (AppLaunchOrdinalMap::const_iterator it = m.begin(); it != m.end();
+       ++it) {
+    const std::string& id = it->second;
+    if (ntp_hidden_extensions_.count(id) == 0)
+      result++;
+  }
+  return result;
+}