Shell's reset method clears namespace from last %run command.

IPython/core/interactiveshell.py

@@ -1038,10 +1038,8 b' class InteractiveShell(Configurable, Magic):'
         self.user_ns.update(ns)
 
     def reset(self, new_session=True):
-        """Clear all internal namespaces.
-
-        Note that this is much more aggressive than %reset, since it clears
-        fully all namespaces, as well as all input/output lists.
+        """Clear all internal namespaces, and attempt to release references to
+        user objects.
         
         If new_session is True, a new history session will be opened.
         """
@@ -1078,6 +1076,9 b' class InteractiveShell(Configurable, Magic):'
         # Flush the private list of module references kept for script
         # execution protection
         self.clear_main_mod_cache()
+        
+        # Clear out the namespace from the last %run
+        self.new_main_mod()
 
     def reset_selective(self, regex=None):
         """Clear selective variables from internal namespaces based on a

IPython/core/tests/tclass.py

@@ -10,10 +10,11 b' import sys'
 class C(object):
     def __init__(self,name):
         self.name = name
+        self.flush_stdout = sys.stdout.flush
         
     def __del__(self):
         print 'tclass.py: deleting object:',self.name
-        sys.stdout.flush()
+        self.flush_stdout()
 
 try:
     name = sys.argv[1]

IPython/core/tests/test_run.py

@@ -202,5 +202,6 b' class TestMagicRunSimple(tt.TempFileMixin):'
 ARGV 1-: [u'C-first']
 ARGV 1-: [u'C-second']
 tclass.py: deleting object: C-first
+tclass.py: deleting object: C-second
 """
         tt.ipexec_validate(self.fname, out)