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Note that starting with version 1.0.8, there are now two lock buttons in the inventory screen. One locks the armors, the other - the weapons. They allow selective locking - per companion.

In version 1.0.9 MCM support was added, but with that I introduced a bug that causes the file config to not work if you don't have MCM. The only way to disable autoequip in that version is to have MCM installed.
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It is possible for the auto-equipment behavior to be disabled altogether, through a config file. Here's how:

Go to "My Documents\Mount and Blade II Bannerlord\Configs" folder and make a folder "SmallSquadVanguard" in it.
Inside the new folder, make a file "config.txt"

Examples:

To disable auto equipment for armors only:
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auto_equip_armors=false
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To disable auto equipment for weapons only:
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auto_equip_weapons=false
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To disable the auto equipment entirely:
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auto_equip_armors=false
auto_equip_weapons=false
auto_equip_ammo=false
auto_equip_mount=false
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Note that shields are considered weapons by the mod, since they are placed into weapon slots.
You can use whatever combination you want. The settings are loaded when Bannerlord starts.
You can disable or re-enable the auto-equipment at any point of the campaign.
You can also probably use another auto-equipment mod. Should be compatible once this mod's auto-equipment is fully disabled.