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

chrome/browser/extensions/extension_sorting.h

 // 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.
 
 #ifndef CHROME_BROWSER_EXTENSIONS_EXTENSION_SORTING_H_
 #define CHROME_BROWSER_EXTENSIONS_EXTENSION_SORTING_H_
 
 #include <map>
+#include <set>
 #include <string>
 
 #include "base/basictypes.h"
 #include "chrome/browser/extensions/extension_prefs.h"
 #include "chrome/common/extensions/extension.h"
 #include "sync/api/string_ordinal.h"
 
 class ExtensionScopedPrefs;
 class ExtensionServiceInterface;
 class PrefService;
@@ skipping 75 matching lines @@
 
   // Convert the page StringOrdinal value to its integer equivalent. This takes
   // O(# of apps) worst-case.
   int PageStringOrdinalAsInteger(
       const syncer::StringOrdinal& page_ordinal) const;
 
   // Converts the page index integer to its StringOrdinal equivalent. This takes
   // O(# of apps) worst-case.
   syncer::StringOrdinal PageIntegerAsStringOrdinal(size_t page_index);
 
+  // Hidden extensions don't appear in the new tab page.
+  void MarkExtensionAsHidden(const std::string& extension_id);

[tapted, 2013/02/26 03:38:49]

I think the member names need to mention NTP, or they read wrong. E.g.
MarkExtensionAsNTPHidden  here.

Elsewhere:
CountNonHiddenItems -> CountNonNTPHiddenItems
hidden_extensions -> ntp_hidden_extensions_;

WDYT?

[koz (OOO until 15th September), 2013/02/26 03:58:37]

Yep, good point. Done.

+
  private:
   // Unit tests.
   friend class ExtensionSortingDefaultOrdinalsBase;
   friend class ExtensionSortingGetMinOrMaxAppLaunchOrdinalsOnPage;
   friend class ExtensionSortingInitializeWithNoApps;
   friend class ExtensionSortingPageOrdinalMapping;
 
   // An enum used by GetMinOrMaxAppLaunchOrdinalsOnPage to specify which
   // value should be returned.
   enum AppLaunchOrdinalReturn {MIN_ORDINAL, MAX_ORDINAL};
@@ skipping 58 matching lines @@
                           syncer::StringOrdinal* page_ordinal,
                           syncer::StringOrdinal* app_launch_ordinal) const;
 
   // Returns |app_launch_ordinal| if it has no collision in the page specified
   // by |page_ordinal|. Otherwise, returns an ordinal after |app_launch_ordinal|
   // that has no conflict.
   syncer::StringOrdinal ResolveCollision(
       const syncer::StringOrdinal& page_ordinal,
       const syncer::StringOrdinal& app_launch_ordinal) const;
 
+  // Returns the number of non hidden items in |m|.

[tapted, 2013/02/26 03:38:49]

ubernit: "non" -> "non-"

[koz (OOO until 15th September), 2013/02/26 03:58:37]

hahaha ubernit. I love it! Fixed :-)

+  size_t CountNonHiddenItems(const AppLaunchOrdinalMap& m) const;
+
   ExtensionScopedPrefs* extension_scoped_prefs_;  // Weak, owns this instance.
   PrefService* pref_service_;  // Weak.
   ExtensionServiceInterface* extension_service_;  // Weak.
 
   // A map of all the StringOrdinal page ordinals mapping to the collections of
   // app launch ordinals that exist on that page. This is used for mapping
   // StringOrdinals to their Integer equivalent as well as quick lookup of the
   // any collision of on the NTP (icons with the same page and same app launch
   // ordinals). The possiblity of collisions means that a multimap must be used
   // (although the collisions must all be resolved once all the syncing is
   // done).
   // The StringOrdinal is the app launch ordinal and the string is the extension
   // id.
   typedef std::multimap<
       syncer::StringOrdinal, std::string,
     syncer::StringOrdinal::LessThanFn> AppLaunchOrdinalMap;
   // The StringOrdinal is the page ordinal and the AppLaunchOrdinalMap is the
   // contents of that page.
   typedef std::map<
       syncer::StringOrdinal, AppLaunchOrdinalMap,
     syncer::StringOrdinal::LessThanFn> PageOrdinalMap;
   PageOrdinalMap ntp_ordinal_map_;
 
   // Defines the default ordinals.
   AppOrdinalsMap default_ordinals_;
 
+  // The set of extensions that don't appear in the new tab page.
+  std::set<std::string> hidden_extensions_;
+
   DISALLOW_COPY_AND_ASSIGN(ExtensionSorting);
 };
 
 #endif  // CHROME_BROWSER_EXTENSIONS_EXTENSION_SORTING_H_