Technically the GUI files are fragmented into a bunch of nonsense files spread throughout 'My Games\Spring\packages' and 'My Games\Spring\pool'. The nonsense files are part of the incremental update system. You can probably override them with the "use local widgets" option and by putting exactly the right files in 'My Games\Spring\LuaUI\Widgets\...'.
There was a developing wiki page but something has happened to it. Making a new skin will involve downloading this
https://github.com/ZeroK-RTS/Zero-K with git and messing around with the files.
Actually, just to be sure. What are you calling a skin? The layout of the UI is relatively easy to change. Ctrl+F11 can move UI components around and there are many settings options for changing what appears. The widget menu can be opened with F11 to remove entire panels. However, you can break something by poking around in there.