Three sentences:
1) Have you been to Germany?
2) Have you ever been to Germany?
3) Have you been to Germany yet?
1): this is asking about an undefined time period with no expectations. If I ask you with no context, "Have you been to Germany?" I probably mean "during the period of your whole life". But if you first say, "I've been to a lot of countries in the last five years," and I ask, "Have you been to Germany?" then I probably mean within the last five years, since you were talking about that time period.
2) Since I said "ever", this emphasizes that I'm asking about the time period in your entire life. I'm asking if you have been to Germany at least once since you were born. It is the opposite of "I have never been to Germany." (Except in the affirmative, we don't say, "I have ever been to Germany." Instead, we just say that we have been there.)
3) Since I said "yet", this implies that I expect you to go to Germany at some point. Maybe you told me your plan, or maybe I just think you should go there. So I ask if you've been there yet. If you say, "I haven't been there yet," it implies that you are planning to or hope to go there at some point in the future.