Clarify that not all configuration options can be overridden by CLI flags

[novemberborn]

Prompted by @Christilut, it's not entirely clear that not all configurations can be overridden by CLI flags. This line should be updated:

Arguments passed to the CLI will always take precedence over the configuration in package.json.

See https://github.com/avajs/ava/blob/master/docs/06-configuration.md.

[havenchyk]

@novemberborn isn't it better to allow overriding by cli?

[novemberborn]

There's some features that should just be configured once and for all, not constantly tweaked through CLI flags.

[sholladay]

This hasn't been a problem for me, but still seems like a strange limitation. Wouldn't it simplify the code to not special-case the configuration? What's actually gained from doing this?

If the goal is just to encourage people to use best practices, a more prominent suggestion to use package.json in the docs might be a simpler approach. Or a console warning, rather than actually preventing config on the command line.

[itskolli]

@novemberborn I have updated the docs to clarify the usage of CLI options along with options in package.json. Please take a look into this PR #1993

[novemberborn]

Wouldn't it simplify the code to not special-case the configuration?

With say the require option, it makes it easier to know which files are required in which order. Specifying different types of glob patterns on the CLI can easily lead to confusion.