"Why you are here?" I have often heard people using that sentence. [For example:] "Just tell me [...] why you are here and why you are learning English?"
I will explain this step by step, but with "he" instead of "you", to make things clearer. First, we have the normal sentence order for a statement:
He is here.
Now, if you want to transform that into a question, you have to invert the order of the subject and the verb. In other words, the subject and the verb have to change places:
Is he here?
Why is he here?
Now let's look at what happens in indirect speech:
I asked you if he is here.
I asked you why he is here.
I told you why he is here.
That is different from a direct quote:
I asked you, "Why is he here?"
So, if a person says, "Tell me why you are here and why you are learning English," that is indirect speech.