Don't use globals when handling CLI options

[invidian]

Currently, we use methods like viper.AutomaticEnv(), which are global and may cause side-effects like #595.

Also globals should generally be avoided in Go: https://peter.bourgon.org/blog/2017/06/09/theory-of-modern-go.html, as they are difficult to test.

We should re-organize our code, which handles CLI to not use global options.

Ideally CLI code should only take care of reading arguments and flags from the user and pass them to Go structures, which can be then tested for specific behavior.