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And don't just go cleaning mods. Sometimes "dirty edits" are deliberate. If I make a mod that relies on a vanilla property, then I might want to make a dirty edit to maintain that property, especially if it's something that might have been changed in overhaul mods.
edit lol Panda ninja'd me with the dirty mod thing.
Saying that, here's Gopher's tutorial on how to clean the master files. He explains things really well, too.
https://www.youtube.com/watch?v=fw3g_N1jcZQ
Edit: Ninja'd by Goyo.
TES5Edit when you open it you will see a box it will pick up your ESM's and ESP's you have in game just click OK.
Edit: Or right click on widow box remove all and then tick boxes that needed to be cleaned as LOOT states.
Do not clean any that have a message that diry edit are required (LOOT also states this)
This will take time to complete (here on is a patience game)(More mods more time)
Once completed it should all load up on left side just choose any file (except skyrim.esm file) and right click on it.
Look for title 'Apply filter for cleaning' and left click ( this process may take some time depending on how many mods etc.) Nothing happens in page (no crash) just look at very top of page and it will ticking the bytes over.
Once completed the left column items will in colour.
Now using your LOOT list of files with dirty edits on it(2 monitors are great for this)
In TES5Edit now right click on SKYRIM.ESM and go down the list until you find one that is on LOOT list. (Do not clean Skyrim.esm) Or just click on noted esm or esp either work.
Left click on it and find REMOVE IDENTICAL MASTERS records and right click
A box with WARNING in it will appear wait and press OK (this is the only time it will show)
Bottom of right side page you will see it working when completed. Left click on file again and find UNDELETE and DISABLE REFERENCES and right click on that, again it will show bottom right page. You have to do that to all files in same order as written repeat until done.
Exit program and a window box will show with list of files you have cleaned just OK it all done for this.
Load WYRE BASH up this it will find Skyrim and it loads up all esm's and esp's, left click on one of the files There should be a build patch there, mine says rebuild patch (Dull in colour,which means I can't use it) as I have already done it. Sorry you may have to read up on, it's been awhile.
Edit new:- For building Bash Patch Mod
Right click on mod that needs bash patch then hold L/ctrl button down Left/click on all other mods (highlights them) that need bashing, then right click on one of them and look down list for build patch (if already done it will state rebuild patch) just follow prompts after that.
Those list stay in LOOT (noticification only)but a bash patch is in your game. Dirty edits are removed and green 'active' word should be there.
Right click on Bash Mod and find rebuild patch this must be done after every clean.
If not sure there is a help button bottom left of screen
Verify game before cleaning starts
If mods are on some may change scripts and VERIFYING THE GAME will REVERT to ORIGINAL SETTINGS. Once cleaned to do use unless mods cause more issues eg. adding new mods then verify, clean and play
carefull
And as stated some dirty edits are needed and LOOT will issue a message/warning on those.
I would not bother with TES5edit if you only a small amount of ITM/dirty edits. But I do use it a lot to see what the background loader is up to because it can help pin point small and major errors and warnings.
U