Deprecating flakeModule and flakeModules.<name>

[mightyiam]

Continuing from #285

Hrm... so the modules.<class>.<name> option is a superset of the flakeModule and flakeModules.<name> options?

And you are considering deprecating in favor of the former? I would support that.

Is there more discussion to be had on that or would you like me to execute in some way?