Refactor phonons

[ElliottKasoar]

Resolves #310

I think this addresses the remaining items, other than non-diagonal supercells, which will be covered by #320.

To do:

• Add tests for displacement kwargs
• Add tests for paths (@alinelena do you have a suitable, very basic, example input file?)
• Update docs for paths in particular
• Add option to define npoints, rather than hard coded value?

[alinelena]

I have attached two paths.yml we can still discuss the best way to have the info in.

1. is full what comes from seekpath
   
   paths.yaml.txt

2. this is a random path (just second branch from above)
   
   path_a.yml.txt

[alinelena]

this will need a rebase otherwise is fine with me

[ElliottKasoar]

(Rebased)