This is needed for the new profiling of features.

This is done by making it a local optimizer. This change to allow
local optimizer to remove variable in the graph. I allow this only for
variable that aren't used.

In a small test case, it wsa taking 0.6s now it take .1s. In a bigger
test case, it was taking 40s. I didn't rerun it with the opt as it is
too long.

This speed up the opt, as we do less iteration on the graph, as in the
EquilibriumOptimizer add in the current iteration the new node in the
graph. The old opt wasn't doing this and I didn't wanted to duplicate
all those type of code.

[MRG]Conv3d2d

Faster opt

theano-nose theano/tensor/tests/test_blas.py:t_gemm.test0a

Fix test of shape_of_variables and raise a good error to explain that the FunctionGraph interface changed.

Disable the clone in some tests and other place where it should not be done.

Don't make TopoOptimizer profile the validate time as this is not needed.

This lower memory usage and speed up optimization by asking for less merge.

This make Merge Optimzer take 21s instead of 35s in one case.

I think this work correctly in case of revert.