make hiding of initial namespace optional

It is by design that names loaded by startup files, etc.
are hidden from things like `%who`.

But this behavior is pretty surprising, especially since

    ipython -i script.py

and

    %run -i script.py

have different behaviors with respect to the hidden namespace.

Since the current behavior was added at the request of @fperez,
I left the default behavior unchanged,
but added a flag to disable hiding initial variables.

IPython/core/shellapp.py

@@ -163,6 +163,11 b' class InteractiveShellApp(Configurable):'
     
     # Extensions that are always loaded (not configurable)
     default_extensions = List(Unicode, [u'storemagic'], config=False)
+    
+    hide_initial_ns = Bool(True, config=True,
+        help="""Should variables loaded at startup (by startup files, exec_lines, etc.)
+        be hidden from tools like %who?"""
+    )
 
     exec_files = List(Unicode, config=True,
         help="""List of files to run at IPython startup."""
@@ -290,7 +295,8 b' class InteractiveShellApp(Configurable):'
         sys.stderr.flush()
         
         # Hide variables defined here from %who etc.
-        self.shell.user_ns_hidden.update(self.shell.user_ns)
+        if self.hide_initial_ns:
+            self.shell.user_ns_hidden.update(self.shell.user_ns)
 
     def _run_exec_lines(self):
         """Run lines of code in IPythonApp.exec_lines in the user's namespace."""