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Refactor trajectory frame caching, align Dataset-owned state access, fix dataset lifecycle, enforce state vs dataset API boundaries, and introduce System architecture#139

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Copilot wants to merge 10 commits intomasterfrom
copilot/remove-md-frame-cache-and-refactor
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Refactor trajectory frame caching, align Dataset-owned state access, fix dataset lifecycle, enforce state vs dataset API boundaries, and introduce System architecture#139
Copilot wants to merge 10 commits intomasterfrom
copilot/remove-md-frame-cache-and-refactor

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