I love General Stores mod, but some things are baffling. Like books and scrolls saved automatically. Or bottles of wine in the Rawfood list.
Reasons why I made this mod:

• If you put an iron dagger in rawfood the container learned that Item and the next sort sent the iron daggers to the food container. I don't think it was a feature. More like a copy/paste List->ListNew effect.  The learning mode was too confusing. I am distracted by nature and the mod is supposed to help me, not stalk every mistake I make. It was more like a Tamagotchi, occasionally needing a visit to the cistern to hit the clean button.
• Unburden or Store all menus don't respect if an item is from a quest or not. There are 3 quests, one from Farengar, another one from a Dawnstar captain and the Riften wizard that include ingredients. And with the new scripts they will continue to be sent to GS (Store all option only ) . But these are quite specific quests and it's not that hard to deal with them. But with books it's another thing. You buy a Spell along with some materials, do Unburden, go to another vendor, buy the Spell again, etc. You end up with no money, without learning the Spell and with 14 copies in the trunk of the books. The mod is unfriendly with the wizards because the scrolls disappear. And with other players too. Oh, there are some skeletons. Let's see if I can finish J'zargo's experiment. Sorry, the scrolls are gone.
• The books list include Black Books, Elder scrolls, Power of elements and Oghma Infinium. Which can break quests. In the Dwanguard quest that requires the Elder Scroll Dragon if you have it in GS it will create the quest to buy it back from Urag even if you never sold it to him. I think I was able to sell it to him to buy it back. Getting it back from GS is not enough.
• With the infinity of CC and Nexus mods adding thousands of items the GS lists are clearly obsolete. Making patches is an impossible task, no 2 players have the same collection of mods. And you can't depend on GS learning mode. After hours of training, one mistake and you have to clean up and start all over again. Using FLM lists you can lose hours too but you don't have to start from scratch every time. And the learning function is clearly secondary or the main lists would have been empty from the beginning.
  

What does this mod do?

• Totally cleans up these lists:
  

• Change the xGSxOneButtonRinseScript and xGSxSortingChest scripts. The Unburden action excludes books, scrolls and "News" (learned) items. It only processes Rawfood, Ingredients, filled GranSoul Gems and craft materials. In the specific menus «Store all» (Food, alchemy etc) the functionality is maintained. (If you still want to automatically store the iron daggers in RawFood go to Pantry and select "Store All".) 
• The sorting chest starts processing the original lists and then the added lists. Originally, several "New" lists were processed before some original ones creating a mess. 
• With empty lists, What is this for? This is where Form List Manipulator comes in. It allows you to add items to lists using configuration files. The xEdit script generates the lists with the following criteria:
  

• Weapons, Potions, Food, Spells, Arrows, Ingredients are processed by each group (Signature) and subclassed following the KeyWords and in the case of armors also "BOD2Armor Type". 
• Ingredients that are also used in cooking recipes (cookpot, Oven, Campfire) are added to xGSxAlchCookFLST (Spices). Meals that are ingredients of another recipe are added to xGSxFoodRawFLST.
• Miscellaneous are added to the Tanning, Constructions etc containers if any recipe of this class uses them. 
• There are mods that have recipes using Lockpicks, Torchs or Currency. They are excluded from the lists.
  

Compatibility
The mod is an ESP, with ESL flag, and only contains empty lists. So almost by definition it can't be incompatible with anything. It can break things, if you don't have FLM installed or it's not active. I personally use General Stores - Bugfix Patch and Cloud storage (the optional mod in GS). GSbugfix adds a functionality to xGSxSortingChest that I stole from it and is included in my version of the script. The main difference is the order in which the items are processed. If you want the semi random order then use the original or bugfix version. Cloud storage does make a change to the list of materials but that is not necessary. The xEdit script GeneralStoresFLMPatch.pas identifies all items used in any recipe.
Installation and configuration
I use MO2 and I don't know anything about Vortex or other things. You install and that's it. In MO2, in the left panel this mod has to be under other mods that modify the behavior of General Stores (like General Stores - Bugfix Patch) for the scripts to work. In the plugins panel it must be below mods that alter GS lists.
The FLM.ini included are specific to my installation. I follow STEP recommendations more or less (I don't use Complete Alchemy and Cooking Overhaul for example). The included inis may work for others as is, if someone doesn't have a mod from my list, FLM ignores it without causing any problems. But it is better to have FLM.ini synchronized with the mods you have. 

Steps to create the FLM.inis:

• Copy GeneralStoresFLMPatch.pas to the xEdit scripts folder.
• Run xEdit and select all the mods and all the groups (image).
• Righ click on anything on the left, select "Apply Script", choose GeneralStoresFLMPatch.pas and accept.
• A dialog box will appear to select the folder where the script will put the files. Choose a folder and accept.
• Depending on how many mods you have and the power of the PC this will take more or less time. My PC is quite powerful and the process takes ~30seconds. I believe that in any case it should be less than 2 minutes.
•  Go to the chosen folder and move all generated GeneralStoresFLMPatch_****_FLM.ini files to the mod folder (overwrite them).
  

The _FLM_ini files can be in other locations and can have any name as long as you preserve _FLM_ini at the end. More information on the FLM page.
The script generates 8 files, one for each type of object. The content of each file is similar. Eg: 
; 000C8866 Small Dwemer Plate Metal~Skyrim.esm; Dwemer Small Plate Metal~Weapons Armor Clothing & Clutter Fixes.esp.
FormList =0xA6DB9~GeneralStores.esm|0xC8866~Skyrim.esm
FormList =0x1018B~GeneralStores.esm|0xC8866~Skyrim.esm
The first line is a comment with the full formid of the item, the original name and the mod, followed by the name and the mod that overwrites it if the name changes. The second name is what you will see in the game but the original name is useful if you are going to look it up on a wiki. The formid to find it quickly in xEdit.
The next 2 lines tell the FLM engine to add this Dwemer clutter to the list xGSxAllSmithFLST (All craft, Unburden) and to xGSxSmeltingFLST (Smelting Items) Probably the recipe comes from Complete Crafting Overhaul Remastered.

Enjoy!