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I assume that you don't see that the first two of your sentences above refer to a question in the person's mind, and the third is an assertion that someone told him the answer.
A phrase is not a single semantic structure if it plays a different semantic role - one in a question and the other in a statement, otherwise any sentence which could be translated into a question would be a question while, by an intelligent definition, it is not.
"Your name is Clark". I know this. It is not a question, indirect or otherwise.
"Your name is Clark?" is a question.
The "semantic structure argument" is either meaningless, or you have not presented it faithfully.
Could you give me an authoritative reference that states that simple indicative statements like "He told me where the keys were" is a question?
Your proposition that such a direct statement is an indirect question is outside my field of experience, and I find it pointless to argue that black isn't white unless you give me some good and well-argued reason to believe that it just might be.
Can anyone tell me what the word "about" is doing in this sentence?
The "what" is just a preposition standing in for those later-mentioned books; it's not an embedded question at all.
All these above given examples are indiect questions.
" What time is it? What have you done? What do you want? are direct questions. We can use them in reported speach but I don't think they are indirect questions. They are simply questions used in reported speech.
I'd like to hear other native speakers' opinions.
I now understand that you are not claiming that "He told me what the matter was." and the OP's sentence are indirect questions.
That was my only argument. We now seem to agree.