[영어Q&A] here vs in here

A1.

It is correct to say "in here" when you enter a room or building, somewhere inside.  

It's cold in here.
It's dark in there.
It's pretty in here.
He in there. (pointing to the door of a room)

By just using the word "here", you can be talking about a general location, not usually inside but it could be inside.  
Wow! It's cold here. (in Alaska)
Why are you here? (why are you present?)
Why are you in here? (why aren't you outside?)

Normally when we are specifically talking about the interior location of something or someone, we say "in here".

I hope this helps.

A2.

I would say the difference is somewhat subtle.

What are you doing here? -- This one asks what you are doing here (in general). Why did you come to the party? What do you want? Example: I didn't expect you to be anywhere near me, but you show up. I'm more concerned about your general presence than your precise location. So, why here instead of somewhere else?

What are you doing in here? -- This one ask specifically what you're doing IN THIS ROOM. It probably means that I didn't expect you to be here in this very room. Example: I invited you to a party at my house, so I expect you to be in my house for the part. I happen to walk into my office and see you going through my files. What are you doing IN HERE? I expect you to be in my house for the party, but I didn't expect you to specifically be in this room.

The difference is basically about where you expect someone to be and NOT to be. If it's cold, you expect someone to be inside. If you're a male in a male restroom, you expect only to see men in the restroom. If you work in an office with confidential information, you don't expect to see people without proper clearance in that office. In all of these cases, you'd use the IN HERE version of the sentence.

Clearer?

A3.

Charmedboi82(A2) has made a limited, but very valid point, as the examples provided demonstrate. In such instances expectations are relevant.

In Charmedboi82's examples there is the supposition that the individual is somewhere without proper permission or in an unwelcome and unexpected capacity, and in those instances, what is said is correct.

Jacinta's(A1) explanation is also correct, but could be broadened. We can also use "in here" at other times than just when entering. For example, we might run into a friend who claims to hate reading in the library, laugh and say "What are you doing in here?" The intent is not always guarded and hostile. Or we might check out the activities in one of a number of workshops :"What are you doing in here?" This information would help us decide which one we want to attend.

Finally, (and maybe someone said this already) "doing here" is more general and can be used interchangeably with the more specific "in here" in most situation. "In here", "out here", "over here", "down here", "up here", etc. are obviously all more specific.

A4.

Please note that although most of charmedboi82's examples dealt with unauthorized entry, his explanation simply used the word "expect." Each of his examples was consistent with the use of "in here" in relation to an enclosed area.  

Whether the question uses "here" or "in here," it expresses surprise. Either version can be used in an enclosed area, but in an open area, "here" would be used rather than "in here."  

When the surprise is a pleasant one, "here" is more commonly used than "in here," even in an enclosed area. Charmedboi82 is correct in noting that "in here" can convey hostility--but it does not always.

Where "here" is used rather than "in here," one must rely on the intonation.
If "What" is stressed, the question is hostile. If "you" or "here" is stressed, the intent is still ambiguous until the facial expression and other body language have been evaluated.