With Garrysmod, materials, models, and sounds in different addons folders are flattened into one global folder (for each) on the website, because of the way this mod was designed. When the same file occurs in the same place in multiple addons folders, it has to have the same contents, or it will be recopied every time because the system sees that the one on the webhosting is different from one of those versions.
To prevent the copying operation from being repeated, duplicate files in different "addons" folders will need to be deleted or made to match exactly. Additionally, you must make certain that all of your folders and files are lowercase, as case matters on the webhosting machine and it looks specifically for "materials", "models" and "sounds" in lowercase letters.
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