Cleanup of `data` directory.

[ijpulidos]

It has been reported in #1063 that some of the examples and data files in the perses/data directory might be broken. We should try to clean this directory and make it have only the files that are needed as data input files for perses. In my opinion it shouldn't have examples or monolithic scripts that are not part of the perses API.

Namely, Tyk2_ligands_example, cdk2-example, bace-example, 8mer-example are some of the examples subdirectories that should be cleaned up and moved to the examples directory.