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[Core][2/N] Model runner refactoring part 2. Combine prepare prefill / decode to a single API (#4681)

This PR combines prepare_prompt and prepare_decode into a single API. This PR also coelsce the attn metadata for prefill/decode to a single class and allow to slice them when running attn backend.

It also refactors subquery_start_loc which was not refactored in the previous PR