Xcode 13.3 beta 3: “swift package init” shows warning: “~/Library/org.swift.swiftpm/collections.json has been deprecated” but dunno how to use new one

I faced this problem after I installed Xcode 14.0.
Deleting org.swift.swiftpm worked for me:

1. Make sure that anything related to SPM is not running including Xcode. Close them all before you delete anything.

2. Go to directory and delete the entire org.swift.swiftpm directory (Not only collection directory, but the whole org.swift.swiftpm directory) and if there is also a org.swift.swiftpm.lock, delete that one as well.