diff --git a/IPython/Prompts.py b/IPython/Prompts.py
index 343fb1e..21f1086 100644
--- a/IPython/Prompts.py
+++ b/IPython/Prompts.py
@@ -126,9 +126,13 @@ prompt_specials_color = {
     # Just the prompt counter number, WITHOUT any coloring wrappers, so users
     # can get numbers displayed in whatever color they want.
     r'\N': '${self.cache.prompt_count}',
+
     # Prompt/history count, with the actual digits replaced by dots.  Used
     # mainly in continuation prompts (prompt_in2)
+    #r'\D': '${"."*len(str(self.cache.prompt_count))}',
+    # More robust form of the above expression, that uses __builtins__
     r'\D': '${"."*__builtins__.len(__builtins__.str(self.cache.prompt_count))}',
+
     # Current working directory
     r'\w': '${os.getcwd()}',
     # Current time
diff --git a/IPython/testing/plugin/ipdoctest.py b/IPython/testing/plugin/ipdoctest.py
index 617de83..734afdf 100644
--- a/IPython/testing/plugin/ipdoctest.py
+++ b/IPython/testing/plugin/ipdoctest.py
@@ -84,9 +84,19 @@ def _run_ns_sync(self,arg_s,runner=None):
     This is strictly needed for running doctests that call %run.
     """
 
-    finder = py_file_finder(_run_ns_sync.test_filename)
+    # When tests call %run directly (not via doctest) these function attributes
+    # are not set
+    try:
+        fname = _run_ns_sync.test_filename
+    except AttributeError:
+        fname = arg_s
+
+    finder = py_file_finder(fname)
     out = _ip.IP.magic_run_ori(arg_s,runner,finder)
-    _run_ns_sync.test_globs.update(_ip.user_ns)
+    
+    # Simliarly, there is no test_globs when a test is NOT a doctest
+    if hasattr(_run_ns_sync,'test_globs'):
+        _run_ns_sync.test_globs.update(_ip.user_ns)
     return out
 
 
diff --git a/IPython/tests/test_magic.py b/IPython/tests/test_magic.py
index da5a498..7a01728 100644
--- a/IPython/tests/test_magic.py
+++ b/IPython/tests/test_magic.py
@@ -12,7 +12,6 @@ import nose.tools as nt
 
 # From our own code
 from IPython.testing import decorators as dec
-
 #-----------------------------------------------------------------------------
 # Test functions begin
 
@@ -64,6 +63,59 @@ def doctest_hist_f():
     In [11]: %history -n -f $tfile 3
     """
 
+def doctest_run_builtins():
+    """Check that %run doesn't damage __builtins__ via a doctest.
+
+    This is similar to the test_run_builtins, but I want *both* forms of the
+    test to catch any possible glitches in our testing machinery, since that
+    modifies %run somewhat.  So for this, we have both a normal test (below)
+    and a doctest (this one).
+
+    In [1]: import tempfile
+
+    In [2]: bid1 = id(__builtins__)
+
+    In [3]: f = tempfile.NamedTemporaryFile()
+
+    In [4]: f.write('pass\\n')
+
+    In [5]: f.flush()
+
+    In [6]: print 'B1:',type(__builtins__)
+    B1: <type 'module'>
+
+    In [7]: %run $f.name
+
+    In [8]: bid2 = id(__builtins__)
+
+    In [9]: print 'B2:',type(__builtins__)
+    B2: <type 'module'>
+
+    In [10]: bid1 == bid2
+    Out[10]: True
+    """
+
+def test_run_builtins():
+    """Check that %run doesn't damage __builtins__ """
+    import sys
+    import tempfile
+    import types
+
+    # Make an empty file and put 'pass' in it
+    f = tempfile.NamedTemporaryFile()
+    f.write('pass\n')
+    f.flush()
+
+    # Our first test is that the id of __builtins__ is not modified by %run
+    bid1 = id(__builtins__)
+    _ip.magic('run %s' % f.name)
+    bid2 = id(__builtins__)
+    yield nt.assert_equals,bid1,bid2
+    # However, the above could pass if __builtins__ was already modified to be
+    # a dict (it should be a module) by a previous use of %run.  So we also
+    # check explicitly that it really is a module:
+    yield nt.assert_equals,type(__builtins__),type(sys)
+    
 
 def doctest_hist_r():
     """Test %hist -r