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The Assembly Halo's interactions currently are:

• right-click crafting table segment: Open crafting table interface
• right-click other segments: Store last crafting recipe or craft that item
• shift + (right or left) click a segment: clear that segment, if it's not the crafting segment
• shift + right-click crafting table segment: same as without shift
• shift + left-click crafting table segment: no effect

The Manufacturing Halo doesn't appear to modify these click interactions. Seems like it could repurpose one of the shift click actions on the crafting table segment to toggle auto-crafting. For consistency with other toggled items that should probably be shift + right-click, even though shift + left-click is not used.

I have it (in my personal tweaks project) set it to be toggled via right click in the inventory, like the stone of temp, so I'll suggest that approach plus the sneak right click whilst just aiming to the crafting table segment for consistency as you said

The toggle is implemented as suggested (either right-click on the item in the inventory, or shift + right-click on the crafting table segment), with an indicator in the item tooltip and changing color of the rendered segment backgrounds (Assembly Halo blue = disabled, Manufactory Halo cyan = enabled). The only thing still missing is a proper visual indicator in the item's icon. I had an idea for a "programmer art" placeholder texture for the disabled halo, but didn't want to potentially break resource packs, so it's not included yet.

A better item texture for the active/inactive states from someone actually versed with texture creation would be nice.