fix keys directory

[mortezasaki]

The keys are not in the certificate directory

[minrk]

I think the directories are doing what they mean to (there's the original certificates directory, whose contents are populated by the generate_certificates utility, but that is reorganized into sibling private/public key dirs).

If anything's missing, it's perhaps the removal of the temporary certificates directory, which is empty after running generate_certificates.py. What do you think?

[mortezasaki]

I agree with what you say. The certificates directory is empty after executing generate_certificates.py, and the public and private directories are created outside of this directory.

[minrk]

If you want to update the PR to remove the empty dir instead, I'd be happy to merge.