add the header_dirs in the hard part of the key.

NEWS.txt

@@ -16,6 +16,9 @@ Since 0.5rc2
    This do use change the default, but if you used this flags, it was ignored
    for module already compiled.
  * The Theano flag "nvcc.fastmath" is now also used for the cuda_ndarray.cu file.
+ * Add the header_dirs to the hard part of the compilation key. This is
+   currently used only by cuda, but if we use library that are only headers,
+   this can be useful.
 
 =============
 Release Notes

theano/gof/cc.py

@@ -801,7 +801,8 @@ class CLinker(link.Linker):
         The key returned by this function is of the form (version, signature)
         The signature has the following form:
         {{{
-            'CLinker.cmodule_key', compilation args, libraries, config md5,
+            'CLinker.cmodule_key', compilation args, libraries,
+            header_dirs, config md5,
             (op0, input_signature0, output_signature0),
             (op1, input_signature1, output_signature1),
             ...
@@ -861,11 +862,12 @@ class CLinker(link.Linker):
         """
         return self.cmodule_key_(self.env, self.no_recycling,
                           compile_args=self.compile_args(),
-                          libraries=self.libraries()
+                          libraries=self.libraries(),
+                          header_dirs=self.header_dirs(),
                           )
     @staticmethod
     def cmodule_key_(env, no_recycling, compile_args=[], libraries=[],
-            insert_config_md5=True):
+                     header_dirs=[], insert_config_md5=True):
         """
         Do the actual computation of cmodule_key in a static method
         to allow it to be reused in scalar.Composite.__eq__
@@ -895,6 +897,11 @@ class CLinker(link.Linker):
             args = tuple(args)
             sig.append(args)
 
+        if header_dirs is not None:
+            args = sorted(header_dirs)
+            args = tuple(args)
+            sig.append(args)
+
         # IMPORTANT: The 'md5' prefix is used to isolate the compilation
         # parameters from the rest of the key. If you want to add more key
         # elements, they should be before this md5 hash if and only if they