The arsenal-reset between episodes/Master Levels is slightly bugged with the Samsara mod - it resets ammo, but not weapons (so you end up with 50 Bullets/Mini-Zorch/Blue Mana/whatever, but all the weapons you've accumulated). Also, is it possible to have an alternate version that removes the arsenal reset entirely?
Viewing post in Full Run for WadSmoosh'd GZDoom comments
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?