According to the dev team's blog, KSP, 1.0 is 7 days from launch, and I was wondering, does the game itself auto-update, or do I have to manually download the game again from the website? Please note, this question is NOT about KSP 1.0, I'm simply wondering if the game auto-updates.
According to the FAQ, you have to open the patcher in the game's folder manually.
Start the Patcher located within your game folder manually, it should be the one with the Squad monkey, if you have a Patcher file with a Kerbal icon feel free to delete it. You can also download a fresh up to date copy from the Store following the instructions. If you have the Steam version of the game you don't have to do anything, the Steam client will update your game automatically.
So it looks like it will not auto-update. That being said, I only have experience with the Steam launcher (which does auto-update) so this may be incorrect. If you have mods installed or you don't want to update right away, I'd make a copy of the entire KSP folder and store it somewhere on your computer because you generally can't go wrong with making backups.