Fastest way to clone a github repo to computer without having to delete older versions, just update the changed files?

Question

I'm using Github desktop but whenever I try to sync to get the updated files it tells me syncing would overwrite my uncommited changes (probably the config file) and either to commit or discard them. So I have to delete the whole thing and then put in all my settings back into the config file which wasn't even updated. Is there a better program to do this?