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

chrome/browser/extensions/extension_sorting.h

Index: chrome/browser/extensions/extension_sorting.h
diff --git a/chrome/browser/extensions/extension_sorting.h b/chrome/browser/extensions/extension_sorting.h
index a661bf058a0d19d29493302ba041dbdc2c6145bc..5efedfa115f5c8bb195c23eb0c87760efb15b6d4 100644
--- a/chrome/browser/extensions/extension_sorting.h
+++ b/chrome/browser/extensions/extension_sorting.h
@@ -6,6 +6,7 @@
 #define CHROME_BROWSER_EXTENSIONS_EXTENSION_SORTING_H_
 
 #include <map>
+#include <set>
 #include <string>
 
 #include "base/basictypes.h"
@@ -101,6 +102,9 @@ class ExtensionSorting {
   // 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;
@@ -179,6 +183,9 @@ class ExtensionSorting {
       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.
@@ -205,6 +212,9 @@ class ExtensionSorting {
   // 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);
 };