Add session offset to history manager's reset method.

IPython/core/history.py

@@ -285,6 +285,8 b' class HistoryManager(object):'
         self.output_hist.clear()
         # The directory history can't be completely empty
         self.dir_hist[:] = [os.getcwd()]
+        # Reset session offset to -1, so next command counts as #1
+        self.session_offset = -1
 
 class HistorySaveThread(threading.Thread):
     """This thread makes IPython save history periodically.