Missing deallocations

--- Description edited to update and clarify intent ---

This MR adds deallocations in several parts of the code that never deallocated module arrays.

While it's true that arrays are destroyed/derreferenced when SIESTA ends, this was bringing me headaches when using valgrind to track a memory leak.

I took the chance to standardize most of the routine names that deallocate arrays in a module to _reset.