Update phono3py file parsing and phonon transport example files

[jcoulter12]

A pull request doing three small things:

Updating the file parser for phonopy/phono3py files.

• Dimension of supercell is now read from phonon_supercell_matrix and supercell_matrix rather than dim/dim_fc2 from yaml files. When using the command line interface, the latter are not written, and Phoebe cannot read the files (such as for the case of the ML force field -> thermal conductivity tutorial).
• Long term fix to avoid ongoing problems with this would be to address issue Change phonopy input parsing to use a YAML library #161

Updating the phonon transport example files

• The phonon transport example files were quite out of date (2 years old). I added an example for phono3py thermal conductivity in addition to the existing ShengBTE files.
• Additionally, I removed a now unused disp.yaml file from the test data.

Updating citation information to point to the now-published manuscript