Support directories in entry_paths

[eimrek]

At the moment, we only support files as entry paths:

entry_paths:
      - file: structures.zip
        matches: ["*.cif"]

but a nice and simple use case would be to also support directories here.

This pr allows this. but also renames file: to path: (in a backwards compatible way).

I also added an example: directory_of_cifs.

I think the paper won't be affected much, probably only requires changes in one figure.

[ml-evs]

Sounds good to me, happy to merge as-is but one minor thing might be to keep one of the test cases with the old alias so that we can make sure we only break it in a controlled way in the future? e.g., a test with config_version still at 0.1.0 (I think here all the test cases have been updated?)

[eimrek]

thanks @ml-evs! I kept the zip_of_cifs example with the old alias ;)