Also, remove caddy from docker-compose.

No need to copy .nix files. They are bound by CI anyways.

Also, graphviz and igraph are in separate nix files now.

The problem was caused by the improper usage of
`delegate_ctrl` when creating the coreNLP process. For a long
time I was under the impression this flag was essential to allow child
processes to shutdown cleanly without leaving zombie threads, but the
result here in the context of the testsuite was that the coreNLP server
was receiving the first Ctrl^C, completely starving the Haskell RTS,
which wouldn't receive any and as a result our testsuite would be
running forever.

By default, we shouldn't run debug logs for phylo in production, let
alone some that runs within pure code.

Debug logs will hinder performance, and showing them on the production
server is not their place anyway.