So I've been having this issue with Nexus Mod manager every time I would apply a mod that it would 
add Skyrim.esm twice to the list contained in Plugins.txt.

I've read around the Internet and it seems that quite a few people have had this issue with Nexus 
Mod Manager and for whatever reasons it's something that Nexus has refused to fix.

I got annoyed with having to go in and delete the Skyrim.esm listings myself so I made this .bat 
script that will do it for me.

The Install.bat script moves the SPF.bat file too the Skyrim directory and adds the Skryim directory 
to the PATH variable so that SPF.bat can be run from anywhere through either the command line or just 
from the start menu search.

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/Instructions/
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1) Run install.bat
Note: Edit the variable skydir to be the directory containing Skryim
The default is currently C:Program Files (x86)SteamSteamAppscommonSkyrim

2) Type in SPF in either the windows search or command prompt and it will fix plugins.txt

3) That's it, the game should run fine now without the plugins.txt error created by Nexus Mod Manager