This is how it should look like →

Cutting lines file

This layer should be used to cut the board.

• I am not sure about the lines thickness. They should allow a student to break the board easily.
• The holes should be M3

Copper bottom file

This layer should be added to the bottom copper layer.

Silk Screen Top file

This is the top silk screen layer

Solder mask file

This is the one I'm a bit confused about.

It should flash out the top copper layer. It's not connected to any component. It's only for educational purposes.

The black lines should be copper, and the white should be black.

This (I think) should be used as the solder mask layer, so you could see the copper where the black lines are.

Copper file

This is the top copper layer, but I don't think it's needed.