Let's consider the following context:
You come to the office on Saturday and see somebody finish some
actions and now (s)he is sitting at your workplace (you didn't expect
to meet anyone), but anyway you are not surprised and just want to
know what's happened.
There are at least two ways to ask your colleague:
What were you doing here?
What have you been doing here?
According to the rules I've learned, there is no big difference between these options.
Of course, our choice could depend on what my colleague is doing when I ask or other rules I don't know, but I do want to know what native speaker feels comparing these two questions in the above context and what the difference is.
Best Answer
In the case of the present perfect continuous, the action is still going on, but you consider the past portion of it. Example: Your colleague is on your computer doing something and you ask: ''What have you been doing here''?
In the case of the past progressive, the action was going on in the past. Example: Your colleague is sitting on your workplace. He turned off the computer and was about to leave when you arrived and asked: ''What were you doing here?''
In the case of the present progressive, as you indicated it in the title, the action is going on in the present/right now. Example: Your colleague is doing something on your computer and you ask: ''What are you doing here?''
So, the answer depends on what your colleague is doing at the moment you ask this question and what portion of time you consider.