In response to post #9270404. #9277005, #9280302, #9285270, #9287387, #9289637, #9290252, #9291670, #9293307, #9294485, #9297315, #9298785, #9299077 are all replies on the same post.
Ooops - I didn't mean to recommend moving SUM.esp out to a new mod or even the SUM Mod itself as I had done. I only mentioned that SUM.esp stayed in the SUM Mod I moved it to as a contrast to the other folders that SUM creates for me which don't get moved.
With SUM, I'd still recommend leaving everything it creates / generates in Overwrite, mainly for simplicity's sake. So, I'm bascially agreeing with wolverine2710.
The only two cases where I am deviating from that is I've moved out those cleaned .esm files and the general patch .esp as well as my TES5Edit backups into separate new Mods. I did that because I knew I wouldn't be modifying those in future, and wanted to keep Overwrite limited to things I know will be overwritten fairly often.
Also, since you've mentioned that you saw the Meta.ini files in MO's mod folders, I want to ask if you are moving files around in Windows rather than in MO itself?
I ask this because based on Tannin's change release notes and also his comments on his Issue Tracker, it seems that it is not a good idea to move files around in the ModOrganizer directory unless you absolutely have to.
MO's interface allows you to create folders, and delete, rename, and move files around within each mod. You can't move files between mods except for Overwrite. Since MO version 0.99.0, Tannin has had the feature to move files out of overwrite, either to a "new" mod, or an existing installed mod.
Only in a few cases do you need to go out to windows to move things around, for example in Neovalen's Skyrim Revisted Guide, some cleaned .esm files need to get moved into \ModOrganizer\overwrite. But generally I would recommend to avoid moving files around in Windows - again, I've based this idea on Tannin's notes and comments. Apparently, MO keeps track of files in memory, and if you move things around while it's running, things could not work as expected.
Anyhow, let's see about those files you've listed:
I googled and these are generated by SKSE plugins for two mods: HDT Physics Extension, and Enhanced Character Edit.
Although SKSE itself should not be installed through MO as a mod, MO of course is designed to see that SKSE is installed and add it to the list of executables that you can launch through MO so they recognize the virtual Skyrim \data tree that MO creates.
However, you can (and probably should) install SKSE's \scripts folder as a Mod in MO. In this case you would would want to download the .7z archive of SKSE (not the installed), and then only copy SKSE's .exe and .dll files directly in Windows into the main \Skyrim directory. Then you would "manually" install SKSE's script folder as a mod in MO, by clicking on the "Install a new mod" button in the upper-left corner of MO. You'll get the simple install interface - just deselect everything except for /scripts, making sure that it displays like this:
. + \scripts
Then, MO allows you to install SKSE plugins as mods, which is what you should do. I think HDT Physics Extensions is just a SKSE plugin, so you'd download the archive and install it in the same way as I've describe here for the SKSE \scripts directory.
This gives you the flexibility to simply disable your SKSE plugin mods for testing and troubleshooting.
Your SKSE plugin .log files showed up in Overwrite because they were probably installed "outside" MO, I am guessing, which won't break anything - but I'd still recommend installing them "within" MO for better control and flexibility.
If you install SKSE plugins through MO, then they should hopefully write the .log file into MO's mod folder for that plugin. I have SKSE -Elys- AltF4 installed through MO, for example, and the .log file for that is written in that Mod folder, and not in Overwrite. I have noticed that some of my SKSE plugins write their .log file in the main /Skyrim/Data directory, so in that case you will find them in the "real" \Data directory out in Windows. This doesn't hurt anything at all (they're .log files!) so I never worry about it.
If you do try removing your SKSE plugins from your "real" \Data\SKSE\Plugins folder and installing them through MO, and then still see .log files in Overwrite, I would say there's still no reason to be concern about it. They will not affect your game in any way.
These two files must be something that was written by a mod after you started Skyrim. I searched on ATTK UI, and have to say that there's only sketchy information on it - despite being so incredibly popular on Nexus before it was "moved" to a private site.
I am hesitant to install it on my setup to see what it does, but I saw notes about it interacting with SKSE, and a video of the settings window, so if you are running from within MO, then any files that ATTK modifies will land up in the overwrite folder.
I have to guess it creates a blank bgs_Logo.bik file to turn off the Bethesuda opening animation. In this case, I'd suggest deleting it from Overwrite, and then in Windows, navigate to \skyrim\Data\Video, and rename BGS_Logo.bik to BGS_Logo.BAK. That also has the effect of skipping the intro video.
Are you using Customizable Music or Main Menu Randomizer, by chance? Any mod which changes the main menu music theme while running Skyrim would result in mus_maintheme.xwm being written in your overwrite folder.
If the music theme that is there now is the one you want for the rest of time, then you can either move it to it's own mod. If it's part of Main Menu Randomizer, then mus_maintheme.xwm will be written every time you run Skyrim, and it should be left in Overwrite.
Now, wasn't that easy????