Because they are now inside the BSA file, so the old files are not only redundant, but also can lead to unwanted issues (as a file inside a folder blocks the corresponding file in BSA).
Masters for: Streamsave_20.ess00 Oblivion.esm01 EnhancedWeatherSIOnly.esm [Version 1.0.7]02 All Natural Base.esm [Version 0.9.6]03 Francesco's Leveled Creatures-Items Mod.esm04 Francesco's Optional New Items Add-On.esm05 Cobl Main.esm [Version 1.71]06 Oscuro's_Oblivion_Overhaul.esm [Version 1.34]07 Mart's Monster Mod.esm [Version 3.7b3p3]08 CyrodiilUpgradeResourcePack.esm09 TamrielTravellers.esm [Version 1.39c]0A FCOM_Convergence.esm [Version 0.9.9a7]0B Armamentarium.esm [Version 1.3]0C Artifacts.esm0D Kvatch Rebuilt.esm0E AFC v2 Core.esm0F Progress.esm [Version 2.0]10 CustomSpellIcons.esm11 HorseCombatMaster.esm12 Unofficial Oblivion Patch.esp [Version 3.2.0]13 UOP Vampire Aging & Face Fix.esp [Version 1.0.0]14 Oblivion Citadel Door Fix.esp15 DLCShiveringIsles.esp16 Unofficial Shivering Isles Patch.esp [Version 1.4.0]17 Francesco's Optional Chance of Stronger Bosses.esp18 Francesco's Optional Chance of Stronger Enemies.esp19 Francesco's Optional Chance of More Enemies.esp++ FranDarkSeducerWeapFix.esp++ FCOM_Francescos.esp [Version 0.9.9]++ FCOM_FrancescosItemsAddOn.esp [Version 0.9.9]1A FCOM_FrancescosNamedBosses.esp [Version 0.9.9]1B EnhancedWeatherSIOnly.esp [Version 1.0.5]1C All Natural.esp [Version 0.9.6]++ All Natural - EW + NW + AWS.esp [Version 0.9.6]1D phinix-waterfix.esp++ Symphony of Violence.esp1E 300_Lore_Dialogue_Updated.esp1F AliveWaters.esp20 AliveWaters - Koi Addon.esp21 AliveWaters - Slaughterfish Addon.esp22 Ayleid Loot EXtension.esp23 AFC v2 Combat Moves.esp24 AFC v2 Damage Text.esp25 AFC v2 Gauntlet Weaponry.esp26 AFC v2 Locational Damage.esp++ AFC v2 Tempfix.esp++ Item interchange - Extraction.esp [Version 0.76]27 Mage_Guild_Teleport.esp28 Oblivion Cats v0.2b.esp29 Redecoration.esp2A Living Economy - Items.esp2B Enhanced Economy.esp [Version 2.1.2]2C moDem's City Life.esp2D Choices and Consequences.esp2E Landmarks.esp2F Guild Map Markers.esp30 HotkeyCasting.esp31 Lem - Hotkey Cyclers.esp++ MaleBodyReplacerV4.esp32 DMGloves.esp33 PersuasionOverhaul.esp [Version 1.4]34 HorseCommandsSI.esp35 XSPipeMod.esp [Version 1.2]36 Thieves Arsenal.esp++ Slof's Horses Essential.esp37 MD Saddlebags v3.0.esp38 MELF_HorseSanity.esp39 Slof's Oblivion Robe Trader.esp3A Cobl Glue.esp [Version 1.69]3B Cobl Si.esp [Version 1.63]3C OOO 1.32-Cobl.esp [Version 1.69]++ FCOM_Cobl.esp [Version 0.9.9]3D Bob's Armory Oblivion.esp3E FCOM_BobsArmory.esp [Version 0.9.9]3F Loth's Blunt Weapons for Npcs.esp++ FCOM_LothsBluntWeapons.esp [Version 0.9.9]40 Oblivion WarCry EV.esp41 FCOM_WarCry.esp [Version 0.9.9]42 Oscuro's_Oblivion_Overhaul.esp [Version 1.34]43 Choices and Consequences - OOO.esp [Version 0.2]++ ArmamentariumLLVendors.esp44 ArmamentariumArtifacts.esp [Version 1.3]45 OBSE-Storms & Sound SI.esp46 FCOM_Convergence.esp [Version 0.9.9]47 Choices and Consequences - MMM.esp [Version 0.2]++ FCOM_EntropicOrderRebalance.esp [Version 0.9.9beta2]48 FCOM_RealSwords.esp [Version 0.9.9]49 FCOM_DurabilityAndDamage.esp [Version 0.9.9]++ FCOM_SpawnRatesSlightlyReduced.esp [Version 0.9.9]4A Mart's Monster Mod - More Wilderness Life.esp [Version 3.7b3]++ FCOM_SaferRoads.esp [Version 0.9.9]++ FCOM_LessRats.esp [Version 0.9.9]++ FCOM_NoAdventurersInGates.esp [Version 0.9.9]++ FCOM_LessReaversInGates.esp [Version 0.9.9]++ Mart's Monster Mod - Looting NPCs & Creatures.esp [Version 3.7b3]++ Mart's Monster Mod - Less Reavers.esp [Version 3.7b3]++ Mart's Monster Mod - Less Bone Loot.esp [Version 3.7b1]++ Mart's Monster Mod - More Passive Wildlife.esp++ Mart's Monster Mod - Midas Creature Ingredients.esp4B Mart's Monster Mod - Safer Quest Locations.esp [Version 3.7b3]4C Mart's Monster Mod - Zombies for Body Meshes.esp [Version 3.7b1]4D Mart's Monster Mod - Dungeons of MMM.esp [Version 3.7b3]4E Mart's Monster Mod - Gems & Gem Dust.esp [Version 3.7b3]4F Mart's Monster Mod - Hunting & Crafting.esp [Version 3.7b3p3]50 Mart's Monster Mod - Farm Animals.esp51 Mart's Monster Mod - Diverse WaterLife.esp [Version 3.7b3p3]++ Mart's Monster Mod - Slof Horses Complete.esp [Version 3.7b3]++ Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp [Version 3.7b3]++ MMM_Runeskull_Rebalance_BETA2.esp [Version Beta]++ TamrielTravellerAdvScript.esp [Version 1.39c]52 TamrielTravellers4OOO.esp [Version 1.39c]53 TamrielTravellersItemsnpc.esp [Version 1.39c]54 TamrielTravellersItemsCobl.esp [Version 1.39c]55 TamrielTravellersItemsVendor.esp [Version 1.39c]56 ShiveringIsleTravellers.esp [Version 1.39c]++ ShiveringIsleTravellersFriendlyFactions4MMM.esp [Version 1.39c]++ FCOM_TamrielTravelers.esp [Version 0.9.9]++ FCOM_DiverseGuardUnity.esp [Version 0.9.9]++ FCOM_BobsGuardUnity.esp [Version 0.9.9]++ FCOM_HungersUnitySI.esp [Version 0.9.9]++ FCOM_Archery.esp [Version 0.9.9]++ FCOM_FriendlierFactions.esp [Version 0.9.9]57 FCOM_MoreRandomSpawns.esp [Version 0.9.9]58 FCOM_MoreRandomItems.esp [Version 0.9.9]++ Mart's Monster Mod - Shivering Isles.esp++ ArmamentariumLL4OOO.esp [Version 2.0]++ PersuasionOverhaul_OOO.esp [Version 1.2]++ PersuasionOverhaul_MMM.esp [Version 1.2]++ Fransfemale.esp59 SSEE-OOO.esp++ MMM-Cobl.esp [Version 1.69]5A Enhanced Quest Roleplaying.esp++ Enhanced Quest Roleplaying - OOO.esp++ Enhanced Quest Roleplaying - FCOM.esp5B Artifacts.esp5C Kvatch Rebuilt.esp++ Kvatch Rebuilt - OOO Compatibility.esp5D Kvatch Rebuilt - Leveled Guards - FCOM.esp5E TheElderCouncil.esp5F TheElderCouncil_TempleOfTheOne.esp60 VaultsofCyrodiil.esp61 24HrArenaAliveV2Towers.esp62 24HrArenaAliveLow.esp63 The Lost Spires.esp64 Mighty Umbra.esp65 Blood&Mud.esp66 Lost Paladins of the Divines.esp67 Origin of the Mages Guild.esp [Version 5.1]68 TheNecromancer.esp69 Mart's Monster Mod - City Defences.esp [Version 3.7b3p3]++ FCOM_MightyUmbra.esp [Version 0.9.9]6A FCOM_Blood&Mud.esp [Version 0.9.9]++ FCOM_SlofsRobeTrader.esp [Version 0.9.9]6B FCOM_OMG.esp [Version 0.9.9]++ FCOM_OMGSRT.esp [Version 0.9.9]6C road+bridges.esp [Version 4.4]6D Oblivion Gate Map Marker Remover.esp [Version 1.1.0]6E Harvest [Flora].esp [Version 3.0.0]++ Harvest [Flora] - Shivering Isles.esp [Version 3.0.0]++ FewerOBGates.esp6F Mimics!.esp70 Music Controller.esp71 Enhanced Vegetation [125%].esp72 Toggleable Quantity Prompt.esp [Version 3.1.1]73 Alternative Start by Robert Evrae.esp74 RealisticForceMedium.esp75 RealisticMagicForceMedium.esp76 Power Exhaustion.esp [Version -01]77 GalerionUnarmoredAcrobatics.esp78 EnchantmentMastery.esp79 SupremeMagicka.esp [Version 0.89]7A SM_ShiveringIsles.esp [Version 0.86]++ SM_OOO.esp [Version 0.89]++ SM_MMM.esp [Version 0.89]++ SM_COBL.esp7B SM_EnchantStaff.esp [Version 0.80]++ SM_UnlockSpells.esp [Version 0.70]++ SM_Scrolls.esp [Version 0.84]++ SM_SigilStone.esp [Version 0.83]7C MidasSpells.esp7D Midas OscuroGems.esp++ Midas Betterholy.esp7E Syc_AtHomeAlchemy.esp7F RshAlchemy.esp80 Enchantment Enhanced.esp81 attack and hide harder v2.1.esp82 DD_ProximitySneakPenalty.esp83 SM Bounty.esp [Version 1.05]84 ProgressGSD.esp [Version 1.1]85 ProgressMBSP.esp [Version 1.0]86 ProgressSBSP.esp [Version 1.0]87 Legendary Abilities-Fortify Health MOJ.esp88 Grandmaster of Alchemy.esp89 S.P.A.M. 100+.esp8A S.P.A.M. option - Restore Spec.esp8B S.P.A.M. option - Restore Fav.esp8C immersive_caves_manual.esp++ Item interchange - Placement for FCOM.esp [Version 0.76]++ Item interchange - Option, Ingredients in Bulk.esp [Version 0.76]++ Mart's Monster Mod - Resized Races.esp [Version 3.7b1]8D Cobl Races.esp [Version 1.52]** Cobl Races TNR.esp [Version 1.53]** Cobl Races TNR SI.esp [Version 1.53]++ Cobl Races - Balanced.esp [Version 1.52]8E NRB4 Standard Road Record.esp++ Cobl Filter Late MERGE ONLY.esp [Version 1.53]8F Cobl Silent Equip Misc.esp [Version 01]** All Natural - Indoor Weather Filter For Mods.esp90 Bashed Patch, 0.esp91 Mart's Monster Mod - Diverse Runeskulls Loot beta Place After Bashed Patch.esp92 CustomSpellIcons.esp93 CleanQuitAlternative.esp94 FormID Finder4.esp95 VisiblyUnlimited.esp96 Duke Patricks - Friendship Ring For Companion Detection.esp97 Duke Patricks - Near Miss Magic And Arrow Shots Alert The Target.esp98 Duke Patricks - Momentum Damage Bonus Custom.esp99 Duke Patricks - Fresh Kills Now Alert The NPCs.esp9A Duke Patricks - BASIC Script Effect Silencer.esp9B Deadly Reflex 5 - Timed Block with no damage or durability changes.esp9C DeadlyReflex 5 - Combat Moves.esp9D SM_DeadlyReflex.esp [Version 0.86]9E Streamline 3.1.esp