Document that new configuration should use the config file NO CHANGELOG

This has been discussed several times among the maintainers but we neglected to document the outcome of our discussions.

Workhorse configuration uses:

1. Command-line flags
2. An optional configuration file
3. Environment variables

Environment variables are hard to avoid (if only because libraries may use them) but it makes no sense that we have both flags and a file. At this point we cannot justify a project to get rid of the flags, but at least we can reduce confusion by making it clear that new configuration options should go into the file and not into the flags.