Fix preferred versions in resolve dependencies

[zkochan]

about the possibility of overrides in preferredVersions, just noticed in code below(for both - before and after the pr), not sure if that can cause issues:

    if (!newPreferredVersions[resolvedPackage.name]) {
      newPreferredVersions[resolvedPackage.name] = {}
    }
    if (!newPreferredVersions[resolvedPackage.name][resolvedPackage.version]) {
      newPreferredVersions[resolvedPackage.name][resolvedPackage.version] = 'version'
      // ^^ -- here the content of `preferredVersions[resolvedPackage.name][resolvedPackage.version]` is possibly modified
      // that will happen if `resolvedPackage.name` was already in `preferredVersions` ()
    }

Originally posted by @zxbodya in #6735 (comment)