MC-148641/clear does not apply to slots of crafting
The items in slots of your 2x2 or 3x3 crafting table are not impacted by the clear.
Example attached with :
/clear @p stone
2019-04-18, 02:00 PM
2019-04-18, 05:03 PM
2019-04-18, 05:03 PM
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MC-148641