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This pull request fixes duplicate tool-output handling (caused by #2230) so the latest item wins consistently when entries share the same stable identifier (for example call_id). It addresses a regression where older session/history outputs could silently override newer outputs, causing model input and persisted session state to diverge from the latest tool result.
This pull request updates deduplication behavior in runtime paths that prepare model input (call_model_input_filter for both non-streamed and streamed runs) and in session persistence (save_result_to_session), and adds a shared latest-wins helper for internal item deduplication. It also keeps resume and non-resume behavior aligned for orphan tool-call normalization to avoid interruption-dependent context drift.