Because of how config stuff works (by passing in "fake" CLI args), if you try to pass a command line flag that's already configured through oro.kdl, it will error telling you there's duplicate flags.

Instead, we should filter the list of flags-from-config such that we don't try to apply the config one if we have a CLI one already.

Repro steps:

1. Create an oro.kdl file with options { lockfile-only; }, in a basic js project
2. run cargo run -- apply --lockfile-only