Revise dimensions of passing arguments, remove assumed-size arrays and declare INTENTs

[lopeztarifa]

Assumed-shape array like:

real(dp) :: arr(*)

make it harder to follow the dimensions of variables throughout the code. Also INTENT of arguments makes it clear which arguments are inputs or output variables. We should change to declarations like this:

real(dp), dimension(nlec), intent(in) :: arr

[filippi-claudia]

being closed after major refactoring