(Closes #2027) fix for ArrayMixin._effective_shape bug

[arporter]

We had a bug which would cause a crash if we had an array access like a(b) where b is actually an array.

In testing this, I also realised that the ArrayAssignment2LoopsTrans transformation would incorrectly convert something like:

c(:) = a(b)

to

do idx = 1, SIZE(c,1)
   c(idx) = a(b)
end do

This should in fact be:

do idx = 1, SIZE(c,1)
  c(idx) = a(b(idx))
end do

This also means we have a bug in examples/nemo/scripts/utils.py because it should have converted a(b) to a(b(:)).