merge the new Scan change in the trunk.

theano/__init__.py

@@ -69,8 +69,8 @@ FancyModule = Module
 
 from printing import \
     pprint, pp
-import scan as scan_module
-from scan import scan, map, reduce, foldl, foldr, Scan, ScanGrad
+import scan_module
+from scan_module import scan, map, reduce, foldl, foldr, clone
 
 import tensor
 import scalar

theano/compile/function_module.py

@@ -38,6 +38,9 @@ def alias_root(v):
 def view_tree_set(v, treeset):
     """Add to `treeset` all variables that are views of v, given that v is not a view"""
     treeset.add(v)
+    if v.owner and v.owner.op.__class__.__name__ == 'Clone':
+        v = v.owner.inputs[0]
+        treeset.add(v)
     for cl, v_input_pos_to_cl in v.clients:
         if cl == 'output':
             continue