Now that OpenPHT manages & updates skins (thanks BTW - awesome feature!), is it best for me to clear out the old skins, or will OpenPHT just update the previously manually added ones?
When a skin update is available it will show the name with (Update) after it, just select the 'updated skin and it will automatically download and ask you whether you want to use it, the old skin will be removed.
There has been a couple of skin updates over the past couple of days for Aeon Nox and Plex Black Edition, these should be showing as updates in skin selection.
You don’t have to manually move anything
Splendid, thanks for clarifying 
