Okay I've been trying to get Skyproc patchers to work with Mod Organizer. I tried both 32 and 64 bit Java. And I tried right clicking on it in the Data tab and using the Open/Execute as well as the Add as Executable options. I even tried running it from the folder itself. The only way I could get it to work was when I manually copied the files to the actual Skyrim data folder.
This is the error I would recieve.
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skyproc.exceptions.MissingMaster:
DualSheath Redux.esp has some missing masters:
-Skyrim.esm
-Update.esm
Please activate and try again.
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While it would work if I just did a manual install I wanted to keep all my mods in the virtual directory that Mod Organizer uses. That way it keeps my Skyrim folder structure clean.
So here is the fix/work around for those interested in getting skyproc patches to work.
Use a Symlink
I also recommend using SUM Skyproc manager to merge all your skyproc mod installs into. Even if you're only using one skyproc mod, that way if you decide to add another or remove one it makes for easier management.
https://skyrim.nexusmods.com/mods/29865
Open a command prompt and type the following assuming you use default installation paths. Otherwise adjust for your locations.
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mklink "C:\Program Files (x86)\ModOrganizer\mods\SUM - SkyProc Unified Manager\Skyrim.esm" "C:\Program Files (x86)\Steam\steamapps\common\Skyrim\Data\Skyrim.esm"
mklink "C:\Program Files (x86)\ModOrganizer\mods\SUM - SkyProc Unified Manager\Update.esm" "C:\Program Files (x86)\Steam\steamapps\common\Skyrim\Data\Update.esm"
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You can then add the SUM.jar file to your Mod Organizer applications list like normal and it should work.
And don't forget anytime you add,remove,update, shuffle mod order you have to rerun your skyproc patches.
I hope this helps some of you.