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The arsenal resets are done with the "ResetHealth" and "ResetInventory" lines in the mod's mapinfo's entries for the first map of each chapter, ie E2M1, E3M1, E4M1, MAP01, NV_MAP01, TN_MAP01, and PL_MAP01. So you could take those lines out for a no-reset run.

Given that I'm just using a standard mapinfo directive to do it, I'm not really sure how I'd fix mods that break it. Maybe Samsara sets certain weapons to be "never strip this item, even after a ResetInventory"? I believe the Inventory.Undroppable actor flag does this. Are those items normally stripped between Master Levels when playing without the Full Run mod?

They are not - I just checked, and it has that exact flag. Weird.

Thanks for the advice on tweaking the MAPINFO, also