Toying around a bit with your code it seems square_array is never actually called. Checking for an exception directly after the jl_call() reveals a MethodError is raised. This is likely due to the fact that the x argument being passed is an Array{Float64,1} and not a Ptr{Cdouble} (although I don’t know the details of whether that can be made to work when embedding).
Updating the signature of square_array to use x::Vector{Float64} makes the function get called, but array_wrap is then unknown, but is also no longer needed as you can modify the array directly and it will get updated on the C++ side as well.