Does Unity have a Reference folder designation (or something similar)?

Basically, is there a naming convention that is the opposite of Resources? Something where the files contained will NEVER compile into the build? I assume this would be frowned upon since you could still reference it in the project and it would break - but I was curious all the same.

Have a look at the special folder names. If you start a folder name with a dot it will be completely ignored by Unity. However that means Unity won’t import the content at all. The folder won’t even show up in the Unity editor.

If you want a folder where you can actually move assets in the editor and not have them included in a build is currently impossible. Unity’s assetdatabase doesn’t really care about where an asset is located. If it is referenced from any included asset or scene it will be included. Runtime scripts are all together compiled into a single assembly (well not a single one but actually up to two for runtime scripts).

If you need certain assets only inside the editor you may want to move them to the “Editor Default Resources” folder at the root. Though direct referencing an asset would still be possible. However simply using a certain folder name would simplify detecting an unwanted asset that accidentally got referenced somewhere by examine the build protocol in the editor log.