Sorry if I am missing something obvious but I have thought looked for the answer both online and in my head.

Tescosi recommends putting them in a Cleaned Plugins folder in Bash Installers. Presumably the idea is to activate them as a bash package overwriting the dirty versions. This seems to undermine the whole modular basis of Bain. Every plugin then has to be activated in two places. If you uninstall a package or pat of a package you will have to remember to uncheck the right plugins from the Cleaned Plugins package. This sounds messy and liable to cause mistakes.

The alternative is to clean the plugin before creating the Bain package. This means moving the right plugins to data so Tes4edit picks them up, clean them, move them back and then archiving the package. It seems clumsy. Am I missing a better way? I thought synching the package in Bain would be the answer but it is greyed out because Bain doesn't know the file is different.

Thanks in advance

My way is perhaps not the best for all, but it does work for me.

And that is, to create/recreate packages with the new (i.e., cleaned) plugin(s), and store all dirty plugins in one place, out of the way.

Admittedly, it is the way I have always gone about it, which could be the best (only?) reason I continue to do so!

If I were using BAIN to install my mods, I would clean the ESP, then place the original uncleaned ESP in a "Dirty" folder, place the rest of the mod files into a "Data" folder then recreate the archive and save into the BAIN Installers folder for activation. This way I have the original as a backup, but Wrye Bash will only install the clean version.

I tend to clean esps (if they need it) before finalizing BAIN packages. What I do is make a complex package, housing both original and clean esps as shown below:

SomeMod_v1XX

• 00 esp - cleaned
  
• 00 esp - original - Archival
  
• 01 meshes_sound_textures
  
• 10 Docs

Even should the esp not need cleaning I'm tempted to create a complex package consisting of:

SomeMod_v1XX

• 00 esp - pre_cleaned
  
• 01 meshes_sound_textures
  
• 10 Docs

Why? Seeing "00 esp - pre_cleaned" servers as a reminder that the esp has been checked with TES4edit and found OK. Otherwise, at some point down the road I'm apt to question myself.

-Decrepit-

Exactly what I do. It works like a charm

I keep a separate folder tree with a subdirectory for each mod I'm running, organized by subtype, e.g. FCOM components, texture replacers, etc. In each subdirectory I keep a copy of the original download, along with a separate archive containing my final customized version of the archive.

I repackage almost all of my mods before installing them. The repackage typically includes PyFFI'd meshes, cleaned and/or merged ESP files, etc. I only put the files I think I might need into the repackage, e.g. I strip out the documentation I don't want installed in the Data\docs directory as well as any other optional ESP files I know I'll never use. I also tend to just do simple rather than complex archives. This makes my installers tab much cleaner. It's certainly not required to do it this way, and it is more work up front, but I find it makes things much easier if I have to reinstall a package to just click install rather than trying to keep track of which options to check or uncheck. And, if for some reason I decide I need one of those other files I stripped it's easy enough for me to grab it from the original archive.

The only packages I don't repackage tend to be things with complicated BAIN wizards. In that case it's not worth bothering stripping stuff out, other than possibly going through and optimizing meshes.

Now I feel like I'm missing the obvious.

Install BAIN package, which effectively unpacks the mod into Data folder.
Run TES4Edit, clean mod.
Remove the backup esp from Data folder.
Nice clean esp remains..... I see no need to repackage anything.

If there's ever a time I uninstall that mod and want to re-install, I re-clean it.

Oh? Not even to save space? I always repackage everything into a 7z archive to save space. It helps with dealing with the backups.

Not that I'm worried about space, but what space are you saving exactly? You're installing the mod anyway, so install it, then the clean esp overrides the dirty. It's not taking up extra space. Either way, the OP asked for suggestions, that's mine.

Space from the archive.

Sometimes, I've been able to save over 100 MB by redoing an archive to use the 7z format. I have my archives, then I have the installed files in the data folder. I keep the originals around for when I change my install around.

After changing the compression format of the archives on another computer, I ended up saving around a total of 1 - 2 gigs of space. It really does help

My routine is ..

Check the mod is recognised by BOSS, if not take note of dirty CRC for posting in the BOSS thread (its been a while since I found anything though)

Then clean and repackage the BAIN using the cleaned esp to replace the original - TES4Edit is so reliable these days there's nothing to worry about keeping originals (unless you mess up the cleaning routine ... but thats pretty unlikely once you have done it a few times)

Worst case scenario, download it again and repeat.

The only BAINs which have duplicate (overwritten) esp's for me are the GOTY DLC's. I like to keep the game originals BAIN'ed early in my install order, and have a BAIN with cleaned DLC's overwriting those. Getting those again if needs be would entail re-installing the game disks which is less convenient than grabbing mods esps off the net. Not really necessary though.

And the reason for re-zipping any cleaned ones - Purely for convenience of re-installing the whole game via BAIN quickly to the same state it was before crap happened (hard drive on its way out/new machine/new OS/sneaky new Malware that is so stubborn or advanced it necessitates a reformat of the hard drive etc etc) - Last time I had to do that took me circa 25 minutes to be back where I saved and play on

If you just do an automatic clean, then that works fine, as it doesn't take long. However if you're like me and do a thorough manual clean as well, then you'd really need to ensure the cleaned ESP doesn't get lost. Some ESPs can take hours to thoroughly go over manually.

I repack the cleaned ESP and any PyFFI'd meshes from the mod into a new archive and toss the original. I can't foresee any reason to want the originals laying around taking up space if I'm not going to play them that way.

Before installing the any package I download into BAIN archive. I first extract the esp/esm files and throw them in the data folder and run the cleaning.

If dirty then I clean them and repackage so that only the cleaned plugin ever gets installed. The advantage of this is more concise information from BAIN. If you clean them after installing the package will always be orange.

I toss the dirty plugin and don't look back. (If there is a problem I have a backup of the original archive).

If it passes the cleaning then I delete the plugin and install the downloaded archive with BAIN (if it doesn't need repackaging that is). Some mod makers are trusted and no need to even check ... then there is the rest of you.

Thanks everyone, that's very helpful. My instinct was to repackage the cleaned esps and you have confirmed that I wasn't crazy. At first it seemed painstaking but it has got much faster as I got going. I am finding most packages need repacking - they are either dirty, have meshes which can be pyffied or need some restructuring. I had a similar dilemma with pyffi - doing the whole meshes directory would be much easier but I figured it was better to have a set of packages in perfect shape.

In an ideal world, most modders would pyffi their meshes, clean their plugins, make the mod customizable through an ini, and package it in a BAIN-friendly way.

Here's a shout out to modders who already do this (Arthmoor, Vorians, SWG, wrinklyninja, just to name a few - not an exhaustive list by any standard. I apologize if I skipped your name and you do this). Thanks for making our lives easier