punctuation - Do periods and question marks come inside the quotation mark, or outside?

I am very well aware of punctuation usage difference between American and British usage, but this part confuses me a little.

Example:

A. Why did he ask, "Who are you?"
B. Why did he ask, "Who are you?"?
C. Why did he ask, "Who are you"?

The reason I am confused is because a question is enclosed in a question. Now I know when to put a question mark inside and outside quotation mark:

He asked, "Will you go and jump in the pond?" [a question within a statement]

He really said, "Go jump in the pond"? [a statement within a question]

So, which one of the three options is correct? Same goes for use of the period. Should it be placed inside or outside:

D. He said, "Pluck that flower."
E. He said, "Pluck that flower".
F. He said, "Pluck that flower.".

If I pick the D option, would it also mean that my sentence ended with the enclosed sentence?
If I pick the E option, would it mean that my sentence ended while the enclosed sentence was incomplete?

B. and F. seems awkward. Please help!

Answer

I believe the following rule is used in both American English, and in British English:

If a "wrapping sentence" ends with a quotation,
and if the quotation ends with the same punctuation mark as the wrapper,
then include the punctuation mark within the quotation,
and omit the duplicate punctuation mark outside the quotation.

I said, "No."
Do your kids always ask "Why?"
Jack yelled, "Jill!"

As a computer programmer, I have learned to fastidiously avoid inserting incorrect punctuation into quotations. I would rather shorten a quotation (to omit a conflicting final punctuation mark) than change the punctuation mark at the end of the quotation. My practice conflicts with what most American English teachers teach.

If the wrapping sentence ends with a quotation,
and if the quotation ends with a different punctuation mark than the wrapper,
then omit the punctuation mark within the quotation,
and include the wrapper's punctuation mark outside the quotation.
For example, if I were to quote the previous three quotations:

Did I say "No"?
That's the fifth time your kid has asked "Why"!
Jack said something about "Jill".

Of the choices in the original question, I would prefer (A) and (D).

There are situations where I might use (C) and (E). For example, if the quotations are actually parts of longer sentences that continue past the quotations, then I would prefer (C) and (E).