I learned programming through the web, so I lack a lot of knowledge in basic systems / bash / *nix / I'm not even sure how to call that.
I've googled so many time "learn bash" etc but it's never really what I'm looking for.
I regularly discover tools that are so basic yet so powerful (all things you mention) yet I feel there is a lack of (great) resources online to "learn the basic tools of your CL".