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

chrome/browser/extensions/extension_sorting.cc

Index: chrome/browser/extensions/extension_sorting.cc
diff --git a/chrome/browser/extensions/extension_sorting.cc b/chrome/browser/extensions/extension_sorting.cc
index d5e07db3edc707a900db49221a703db21eb53629..0264de6f8eeebf1281c73cbc1300916412fcf072 100644
--- a/chrome/browser/extensions/extension_sorting.cc
+++ b/chrome/browser/extensions/extension_sorting.cc
@@ -364,7 +364,7 @@ syncer::StringOrdinal ExtensionSorting::GetNaturalAppPageOrdinal() const {
 
   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;
   }
 
@@ -445,6 +445,10 @@ syncer::StringOrdinal ExtensionSorting::PageIntegerAsStringOrdinal(
   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 {
@@ -610,3 +614,14 @@ syncer::StringOrdinal ExtensionSorting::ResolveCollision(
   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;
+}