Theres 1 way I've heard of...but I've never tested it so I dont know if it causes any corruptions or not
step 1. in WinMPQ go to "Options..."
step 2. change the maximum files for new archives to the ammount your mod has (no more, no less)
step 3. put all the modded files in a new folder (the same folder for all of them)
step 4. go to "Mpq"->"Add Folder" then add your folder
step 5. rename all the files adding the correct extensions
step 6. close the archive (make sure you made a unprotected backup first!)
step 7. change the settings on WinMPQ back to normal so your next mod isn't protected (normal maximum files is 1024)
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Sounds interesting I'll try that out.