Replace CLI with configuration file

[nichollsh]

The current command-line interface is confusing and overly complicated. There are too many parameters to reasonably pass into one command.

AGNI should instead use a configuration file, which would also allow the many execution scripts to be merged into a single script, instead having multiple configuration files.

I suggest using the TOML format.
https://docs.julialang.org/en/v1/stdlib/TOML/