To me, this makes the most sense.
-Folder
–Project 1
—File 1
—File 2
I’ll throw out another idea for you to explore 
In the project sidebar (where recent projects are shown ) have only folders and projects. Folders can be multiple deep, e.g.
-Holiday Projects
–Christmas
–Halloween
—Monsters
—Ghosts
-RC Cars
etc
Then, on either the main Easel page, or a new sidebar between the projects sidebar and easel, the file and layers navigation. The sidebars would need to be independently collapsible. I also don’t know if the word “file” is the best descriptor, might be worth investigating graphics programs for something similar. I’m assuming layers would have different bit/cut settings and could be cut by themselves. So the new sidebar would show
-File 1
–layer 1
–layer 2
-File 2
–layer 1
e.g.
Front View
-roughing pass
-detail pass
-drilling pass
Rear View
-detail pass
Since this could be it’s own sidebar, it could be hidden for a simple operation, one file and bit, e.g. the Carvey user, and then expanded for a more power user.