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

Just upgraded to Xcode 13.3 beta 3 (from Xcode 13.2.1) and ran swift package init. It generated a deprecation warning, I have not seen this before:

warning: Usage of /Users/sajjon/Library/org.swift.swiftpm/collections.json has been deprecated. Please delete it and use the new /Users/sajjon/Library/org.swift.swiftpm/configuration/collections.json instead.

But I do not know HOW to "use the new ... instead"? In fact I don't even know how or when org.swift.swiftpm/collections.json was created.

What to do?

Full print:

~/Developer/DeleteMe ⌚ 13:57:37
$ swift package init
2022-02-25 13:57:42.211 xcodebuild[54679:13318505] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionSentinelHostApplications for extension Xcode.DebuggerFoundation.AppExtensionHosts.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-02-25 13:57:42.212 xcodebuild[54679:13318505] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionPointIdentifierToBundleIdentifier for extension Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-02-25 13:57:43.052 xcodebuild[54754:13318823] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionSentinelHostApplications for extension Xcode.DebuggerFoundation.AppExtensionHosts.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-02-25 13:57:43.053 xcodebuild[54754:13318823] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionPointIdentifierToBundleIdentifier for extension Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
warning: Usage of /Users/sajjon/Library/org.swift.swiftpm/collections.json has been deprecated. Please delete it and use the new /Users/sajjon/Library/org.swift.swiftpm/configuration/collections.json instead.
Creating library package: DeleteMe

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.