C:\games\OpenMWMods\Tools\tes3cmd

WARNING: May not work properly with exotic drive setups, such as mdadm. In some circumstances plugins may appear to be modified, but changes will not appear in-game. If this happens, try running tes3cmd such that tes3cmd itself and any plugins you tried to clean or modify are all in the same folder.

How to run TES3CMD to clean a plugin:

Step 1: Download It

Windows users want to use the file from the download link above.

Linux users can get a distro-agnostic binary executable from this link. Be sure to make it executable (chmod +x tes3cmd-0.37w.linux.x86_64)

macOS users download this file.

Once you've downloaded TES3CMD, place it into the data path folder listed above.

Step 2: Run It

Windows

1. Copy the plugin you want to clean into the folder where tes3cmd is
2. Navigate to the folder where tes3cmd is and Shift+Right click the folder to bring up the context menu. Click Open Powershell window here and type the following command, replacing the file name in quotes with the one you’re trying to clean: .\tes3cmd.exe clean "Plugin_Name_Here.esp"
3. When this completes, you'll have a plugin named Clean_Plugin_Name_Here.esp. Copy that into the mod's data path folder and delete the dirty plugin from your Morrowind Data Files folder

That's it!

Linux/macOS

1. Open a terminal
2. Type cd /home/username/games/Morrowind/Data Files, but replace the path with the path where your Morrowind Data Files folder actually is on your computer
3. Copy the plugin you want to clean into this folder (it's just temporary, we'll remove it when we're done with this)
4. Type

   /home/username/games/OpenMWMods/Tools/tes3cmd/tes3cmd-0.37w.linux.x86_64 clean Plugin_Name_Here.esp

   , but replace the path with the actual path to the folder where tes3cmd is on your computer, and the name of the plugin with the plugin you want to clean (macOS users should also change the TES3CMD executable name)
5. When this completes, you'll have a plugin named Clean_Plugin_Name_Here.esp. Copy that into the mod's data path folder and delete the dirty plugin from your Morrowind Data Files folder

That's it!

Further References

Run tes3cmd clean --help for detailed information about how the program cleans.

The official wiki and this reddit post about using tes3cmd.exe with MO2 on Windows are great resources.