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Also, it is not possible to save a template when all soldiers have no items on their person. I wanted to do this to have an easy way to clear all inventories, but it won't save it.
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Just in case you were not aware.
It is possible to work around this problem in the following way:
* Assign soldiers to craft.
* Make sure craft contains no items (shortcut "x" in craft item equip screen, if i remember correct).
* Click the inventory button.
Since the game cannot assign any previously assigned items anymore it will reset the load-out of all soldiers on board of that craft to be empty.
Keep in mind that this does not work when the new "apoc style" soldier equipment is active (the option called: "oxceAlternateCraftEquipmentManagement") since that one was specifically designed to prevent these 'accidents'.