Define a single configuration input file for all the tools.

[yakutovicha]

We need to establish a configuration file that is used by all the tools. Preferably, it should be in YAML format.

The issue should be closed when a complete example is uploaded to the repository.

[yakutovicha]

setup.yaml

leed:
    unit_cell:
    ...
    surface_coordinates:
    bulk_coordinates:
rfactor:
    correspondance:
        ...
search:
        ...