[WIP] Prefill-related logic in input preparation for generation

[zucchini-nlp]

What does this PR do?

Fixes #41863 and fixes #40910

We always have had an imperfect way to infer if we're in prefill or decoding stage, which caused us many bugs in the past. The most reliable way is to check cache position values but it is not compile-compatible and also has an edge case

Recently Manuel merged a PR to split prefill into its own function so now we can benefit from it and know with 100% certainty which stage we're in. This PR adds is_prefill flag to generation input preparation and replaces existing logic with the flag.

Also it adds a test case for the above linked issue

[github-actions]

[For maintainers] Suggested jobs to run (before merge)

run-slow: aria, aya_vision, chameleon, clvp, cohere2_vision, deepseek_vl, deepseek_vl_hybrid, emu3, florence2, fuyu, gemma3, gemma3n, glm4v, glm4v_moe, got_ocr2, granite_speech

[HuggingFaceDocBuilderDev]

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint. The docs are available until 30 days after the last update.

[zucchini-nlp]

Another worm of cans, assisted decoding has no prefill separated out and is causing issues now 😢