Support setting plugins in config files and plugin options in CLI flags

[fabiospampinato]

Currently if plugins and their options are both defined in a config file the CLI works, if they are both defined via CLI flags it works, but if plugins are defined in config files and flags are defined via CLI flags then it doesn't work anymore because the CLI thinks those options are unrecognized.

The best option here is probably doing nothing until an unknown flag is passed and then paying the cost for the discovery of the configs files just to be sure about whether we need to throw an error or not.