Here's an update:

In DNN 6.0 Beta 1, the following deprecated method (found in namespace DotNetNuke.Common.Utilities.FileSystemUtils):

public static void AddFolder(PortalSettings portalSettings, string parentFolder, string newFolder, int storageLocation, Guid uniqueId)

ignores the parentFolder parameter completely resulting in the addition of the new folder as a child of the portal home directory rather than the desired parent.

In CTP2, this method included the following line:

var folderPath = PathUtils.Instance.GetRelativePath(folderMapping.PortalID, parentFolder + newFolder);

In Beta 1, this was changed to:

var folderPath = newFolder;

in order to fix Gemini Issue DNN-15928 in which addition of a new folder would always throw an exception since the GetRelativePath method included a check if the physical folder already existed and intentionally thew a new exception if it did not.

I think the following change (line 429 of Library\Common\Utilities\FileSystemUtils.cs) would address the issue but protective coding should also be added should either parentFolder or newFolder params not end with the required forward slash or otherwise be mis-formatted:

var folderPath = parentFolder + newFolder;

I'll either create a new Gemini issue or ask that DNN-15928 be reopened after testing the modification.

The LinkClick issue is not due to failure to generate the correct LinkClick url from a FileID but rather in a change in the behavior of the LinkClickHandler (FileServerHandler) which will now attempt open any file in a new window following a redirect to the actual file url even if the ForceDownload parameter is set to true. I'll investigate this issue further.