You add the 'in' when the speaker is in a container of some kind (often a room or a house), and the person addressed is outside; but you don't have to - unless the speaker wants the person addressed to come right inside. It works similarly with a different environment - like a swimming pool, a lake, or the sea.
If it's lunchtime, and a mother is calling her children in, 'come here' and 'come in here' are equivalent (because the context supplies the 'in' - assuming they're not going to eat outside). But if she goes to a window while they are playing and shouts 'Come here', it might mean '[You can stay outside, but] come here [by the window, where I can talk to you without shouting]'. If she really wants them to come in, - say, because it's time they did their homework - she should say 'Come in here'. If she doesn't, she may need to say: 'Come here... no, right in.'