Document Apalache config format + options

[thpani]

While addressing https://github.com/informalsystems/quint/issues/1196, I tried to write an Apalache config file, but struggled.

The best documentation I found is this manual section. It documents the principle format, but I had to guess the JSON keys since there is no 1:1 correspondence to CLI flags.

@shonfeder Maybe I missed something and there is documentation of the supported config file options somewhere?

The second thing I struggled with is setting --tuning-options / checker.tuning via the config file, which is passed as a single :-separated key=value string on the CLI, but (at least it seems so) needs to be a nested JSON object in the config file. We should confirm this, and document how to set tuning options via config.