Put the nvcc.flags in the hard part of the Theano keys.

NEWS.txt

@@ -11,6 +11,10 @@ Since 0.5rc2
  * Fix a bug with Gemv and Ger on CPU, when used on vectors with negative
    strides. Data was read from incorrect (and possibly uninitialized)
    memory space. This bug was probably introduced in 0.5rc1.
+ * The Theano flag "nvcc.flags" are now included in the hard part of the key.
+   This mean that now we recompile all modules for each value of "nvcc.flags".
+   This do use change the default, but if you used this flags, it was ignored
+   for module already compiled.
 
 =============
 Release Notes

theano/sandbox/cuda/nvcc_compiler.py

@@ -80,8 +80,8 @@ class NVCC_compiler():
         This args will be received by compile_str() in the preargs paramter.
         They will also be included in the "hard" part of the key module.
         """
-        return []
-#        flags = [flag for flag in config.nvcc.flags.split(' ') if flag]
+        flags = [flag for flag in config.nvcc.flags.split(' ') if flag]
+        return flags
 #        cuda_ndarray_cuh_hash = hash_from_file(
 #            os.path.join(os.path.split(__file__)[0], 'cuda_ndarray.cuh'))
 #        cuda_macro = '-DCUDA_NDARRAY_CUH=' + cuda_ndarray_cuh_hash
@@ -205,7 +205,6 @@ class NVCC_compiler():
             # the -rpath option is not understood by the Microsoft linker
             for rpath in rpaths:
                 cmd.extend(['-Xlinker',','.join(['-rpath',rpath])])
-        cmd.extend([flag for flag in config.nvcc.flags.split(' ') if flag])
         cmd.extend('-I%s'%idir for idir in include_dirs)
         cmd.extend(['-o',lib_filename])
         cmd.append(os.path.split(cppfilename)[-1])