What are the differences in usage and nuances between 现在，正在 and 还在？
现在: Now

A: 你现在在干什么？: What are you doing now?

正在: Currently

B: 我正在做作业。: I am doing homework.

正在is this sentence can be translated to doing something at this particular moment, in English you just add ing at the end for currently doing something, but in Chinese you don't have this, so you use 正在 to express doing something now. 我正在做...becomes "I am doing...", or 我正在读...becomes "I am reading..."

还在: Still

A: 你怎么还在做作业呀!: You are still doing homework?

还pronounced "hai" instead of "huan" in this sentence means still doing something.

还在看书：Still reading, 还在这里: Still here...

Also to mention, 还 can also be pronounced "huan", as in 还钱: Pay debt, 还给我: Give it back, it means to return something, but that's a different context itself. 

I guess to make it clearer, sometimes you don't really need to add 现在 or 正在，you just say "你在干什么？What are you doing?", or "我在做作业。I am doing homework.", it sounds more friendly like when you are talking to a friend. 你现在在干什么？sounds more like when your boss or teacher would ask haha.