fixed overwriting of user-system configuration when not set explicitly

| Q             | A
| ------------- | ---
| Bug fix?      | yes
| New feature?  | no
| BC breaks?    | yes, sections are no longer automatically set
| Deprecations? | no
| Tests pass?   | yes
| Fixed tickets | #12 
| License       | MIT

This fixes the overwriting of user-system configuration with the defaults when passing in the app-config.

Note. profile, resetting and the like are no longer automatically enabled, these must be set explicitly.
Pass-in an empty array to trigger there defaults.