Disentangle overlap matrix and *other matrices*

[zerothi]

Describe the feature

Currently the overlap matrix is associated with some matrices through an extra dimension.

However, this turns out to be relatively problematic down the road when we want only to do stuff on the Hamiltonian.

It however, also possess some nice things because the overlap matrix is explicitly present.

In principle it would be ideal if the overlap matrix is associated through the explicit Overlap object, it will definitely complicate matters, but on the other hand it could implicitly allow different sparsity patterns, as well as streamlining the usage.