Tool gizmo shells are used in the Invention skill to generate perks for use on an augmentable tools.
Using a tool gizmo shell opens an interface allowing you to combine different materials to generate perks. This creates a tool gizmo, which can then be used on an augmented item to give it the perks.
Tool gizmo shells are currently unobtainable as the ability to augment tools wasn't included in the initial Invention release.