I have a few apps that create visible folders in my home directory by default. I would like to hide these folders so I don't have to see them when I open Nemo. I prefer to see only the folders I actually use, such as Documents, Videos, Music, Projects, etc. Making them dotfiles either makes the app freak out because it can't find the folder any longer, or, in one case, the app just creates the folder again the next time it is run. Is there a way to hide these files? Perhaps a way to create some sort of alias so the app could search for a given directory, but be redirected to a dotfile? I'm using Linux Mint 18.3 Cinnamon.
Note: This is not a duplicate of this question, as that ended up being a debate on the usefulness of file hiding in general.