Just use the chain rule. Linear operators are essentially vector fields; they're just linear. This viewpoint makes the application of multivariable calculus very straightforward.
Let $x' = Ax$. Let $\nabla$ be the usual vector derivative (that is, $\partial_x$) and $\nabla'$ be that corresponding to the dimension of $x'$. Let $a$ be a vector, and the chain rule tells us that
$$a \cdot \nabla (F \circ A)(x) = [a \cdot \nabla A(x)] \cdot \nabla' F(x')$$
$A$ is a linear function, so $a \cdot \nabla A(x) = A(a)$, so the result is
$$[A(a) \cdot \nabla'] F(x')$$
You can then evaluate the components by plugging in basis vectors for $a$. In index notation, this yields
$$\sum_{j'} {A_i}^{j'} \partial_{j'} F_{k'}$$
This has two free indices, so the result can be interpreted as a matrix of partial derivatives of the component functions.