Assume

"the burglers" is the subject of the clause.

You might think of it this way:

Form 1: The burglars were who? (Not used much, this is called an echo question.)
Form 2: who the burglars were ("who" moves to the beginning. Not a complete sentence - used only as subordinate clause in another sentence.)
In a complete sentence: It was quite a while before we discovered who the burglars were.
Form 3: Who were the burglars? ("were" - the first verb - the only verb in this case - moves in front of the subject. This is a main clause - an interrogative clause.)

When the verb is not "to be", the first two forms are the same; the third form adds "do" (called "do-support"):

1: You put the pizza where?
2: ... where you put the pizza. (In a complete sentence: I can't imagine where you put the pizza.)
3: Where did you put the pizza?

CJ

so in 2# you wrote "who the burglars were" and this isn't a complete sentence right? I have to add smth in the beginning. It should be "who were the burglars?" if we want to regard it as a complete sentence,(1#) right?

Yes, that's right.

And please check these ones: 2# Who are you? 3# I don't know who you are. 4# Apparently you are a cop.

All are correct.
#2 is a question.
#3 is a statement. The subordinate clause "who you are" does not use inversion, which is correct.
#4 is a statement. It has only one clause, and that clause is not a question, so no inversion should be used. It is correct.

CJ

"in future" for British English. "in the future" for American English.

1. Correct.
2. Wrong. "... what you would like to do ..." is the correct form.
The question part (requiring inversion of "you have" to "have you") is correct. That's the main clause. The second clause is subordinate, so it does not invert "you would" to "would you".
3. Correct with "never". There's no problem using "never" or "ever" with the past perfect tense. (Off topic: "like you" is more idiomatic that "such as you".)

CJ