%reset doesn't reset prompt number.

IPython/core/history.py

@@ -164,15 +164,15 b' class HistoryManager(Configurable):'
     def reset(self, new_session=True):
         """Clear the session history, releasing all object references, and
         optionally open a new session."""
-        if self.session_number:
-            self.end_session()
-        self.input_hist_parsed[:] = [""]
-        self.input_hist_raw[:] = [""]
         self.output_hist.clear()
         # The directory history can't be completely empty
         self.dir_hist[:] = [os.getcwd()]
         
         if new_session:
+            if self.session_number:
+                self.end_session()
+            self.input_hist_parsed[:] = [""]
+            self.input_hist_raw[:] = [""]
             self.new_session()
     
     ## -------------------------------

IPython/core/interactiveshell.py

@@ -1045,12 +1045,12 b' class InteractiveShell(Configurable, Magic):'
         """
         # Clear histories
         self.history_manager.reset(new_session)
+        # Reset counter used to index all histories
+        if new_session:
+            self.execution_count = 1
         
         # Flush cached output items
         self.displayhook.flush()
-
-        # Reset counter used to index all histories
-        self.execution_count = 0
         
         # Restore the user namespaces to minimal usability
         for ns in self.ns_refs_table:

IPython/core/magic.py

@@ -1007,7 +1007,7 b' Currently the magic system has the following functions:\\n"""'
                 del(user_ns[i])
             
         else:                     # Hard reset
-            self.shell.reset(new_session = True)
+            self.shell.reset(new_session = False)