Once I click to run minecraft a small window appears saying "Downloading runtime", then three other folders appear onto my desktop: Game, Native Log, and Runtime. This really annoys me, as I have to keep deleting them after I am done with a session of minecraft. Why is this? It never use to happen before.
It sounds to me like you are running Minecraft.exe directly from your Desktop. The desktop is generally not a good place for executable files, and you shouldn't do that.
To fix your issue, you will have to move your Minecraft.exe somewhere else. I suggest you either move it to
%appdata%\.minecraft, where the rest of the Minecraft files are stored. Or create a new folder somewhere, such as
C:\Games\Minecraft and move it there.
Afterwards, create a shortcut to the exe on your desktop, e.g. by doing Right-Click > Send to > Desktop, or Right-Click dragging the icon and selecting Create Shortcut
You want the older version, they now include the runtime and a few other things. The version you want is the older version which requires Java installed already.
You can get it from here: https://beta.minecraft.net/en/download/
Please note this may change, but I've attached a screenshot to highlight as I had issues finding it since I only glanced for a few minutes.
You can create a bat or sh file that will have the program run into a different directory: Second Reply.
If you don't want to do that, you can symlink the directories.
For me, I had a similar problem with my computer. You can either move the minecraft executable to the
(Check where your Java path is leading to, it shouldn't be heading to your desktop)
Yes, create a folder in C:/!Games and then put in there minecraft. Then right click to create a shortcut which you can use on your desktop. Also if you are bothered by a messy desktop trying using the program fences. It comes with a quick hide tool and other desktop organizing features.