Restore Fernando's fix for the __del__ methods on exit bug.

IPython/core/interactiveshell.py

@@ -819,8 +819,11 b' class InteractiveShell(Configurable, Magic):'
 
         # Similarly, track all namespaces where references can be held and that
         # we can safely clear (so it can NOT include builtin).  This one can be
-        # a simple list.
-        self.ns_refs_table = [ user_ns, user_global_ns, self.user_ns_hidden,
+        # a simple list.  Note that the main execution namespaces, user_ns and
+        # user_global_ns, can NOT be listed here, as clearing them blindly
+        # causes errors in object __del__ methods.  Instead, the reset() method
+        # clears them manually and carefully.
+        self.ns_refs_table = [ self.user_ns_hidden,
                                self.internal_ns, self._main_ns_cache ]
 
     def make_user_namespaces(self, user_ns=None, user_global_ns=None):
@@ -985,6 +988,18 b' class InteractiveShell(Configurable, Magic):'
         # Restore the user namespaces to minimal usability
         for ns in self.ns_refs_table:
             ns.clear()
+
+        # The main execution namespaces must be cleared very carefully,
+        # skipping the deletion of the builtin-related keys, because doing so
+        # would cause errors in many object's __del__ methods.
+        for ns in [self.user_ns, self.user_global_ns]:
+            drop_keys = set(ns.keys())
+            drop_keys.discard('__builtin__')
+            drop_keys.discard('__builtins__')
+            for k in drop_keys:
+                del ns[k]
+                                        
+        # Restore the user namespaces to minimal usability
         self.init_user_ns()
 
         # Restore the default and user aliases