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Ok, the topic is lying a bit. But its a work around that works like multiple layers should do.
Take your favorite encoding and open it in a editor. Now select all glyphs, copy it and paste it to the end of the same encoding file. Now add to every glyph a period.
In fact you have doubled every glyph of your encoding. These gylphs will work as your "layer".
Now you have to open the Groups.txt and use the same trick to assign these new gylphs to your standard glyphs. I have done it with Excel and saved the text as tabulator divided text.
Now you can switch by double clicking on the shape group to get to your new "layer". (Please enable "Double-click to edit neighbor or sahpe gylph group" in the FLS prefs.) If you need more layers, you have to do the same steps again. A three layers encoding would look like this:
The Shape groups file would look like this:
A A. A..
B B. B..
C C. C..
Instead of .. you can use other gylphs like : ; but dont use , (comma)!
So, in the metrics window you can work with the first layer like before. If you need to set some samples to compare your different designs/layers, it should look like this.
BTW. The extension pattern to use a period is a first hack. Adam & Yuri will hopefully find a setup that is compatible with all aspects of FontLab & Phyton. The simplicity of this solution is plausible, the file format of FontLab needs no special treatment to store layers and the format stays compatible to earlier versions.