Automatically add `flake/` prefix to CLI extra `--override-input` args

[shivaraj-bh]

The flake/ prefix is added by default when an override exists in the subflake config (for example, see https://github.com/juspay/services-flake/blob/5ae35569c2594dee7be5be343561fb130941be67/nix/omnix.nix#L6-L10) but not when overriden via the CLI, i.e om ci run <flake_ref> -- --override-input <input> <flake_ref>.

See also srid/nixci#71 for some context on flake/