What: Change cmd/uplink to use scopes
It moves the fields that will be subsumed by scopes into an explicit legacy section and hides their configuration flags.
Why: So that it can read scopes in from files and stuff
* fix bug for setting flag only values in process setup
when the code was changed to directly load values into the config
structs, it was missed that some configuration is only defined
through flags, but can be loaded from config files still.
so, we need to propogate the settings to the flag only values.
* add test for setting propagation
* fix linting error
