Add the possibility of finding a shell radius defining a sphere
which contains the first (intersites) neighbours. This is helpful
when using the `hp.x` code and having a structure containing
onsite Hubbard atoms with different number of neighbours.

The Hubbard parameters can now be initialized simply
by perfoming a nearest neighbour analysis (pymatgen).
Standardization of the lattice and the atomic positions
can also be performed to have all the atoms within the
unit cell (needed for the `pw.x` routine).

Pymatgen does not order the atoms by distance.
There is not apparently any such option in the API.
Folding is then now sepatated from standardization
(the latter could produce larger structures).

The refolding wasn't folding numbers
close numerically to 1, e.g. 0.99999999.
To circumvent the issue, a threshold is set,
and it is possible to control it via input.
Also, now the inputs for nearest neighbours
are not passed via kwargs, but via an explicit
dictionary input, which is then given via kwargs
to the NN class.

The url for pymatgen to generate interlinks
across API packages is added.

A set of methods are added to account for some useful use-cases
where the number of nearest-neighbours are needed or when only
the set of indices and the translation vector are required (the latter
is useful for parsing the Hubbard parameters computed from
first-principles).