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Require the native node owner's content digest instead of borrowing an observation artifact digest, which can identify the containing ASAR. Keep unavailable nodes and their path/provenance/partial facts in the trace, without a false actionable target or native Evidence link. Remove the old fallback and allocate the query index only for eligible native targets. Verify real public CLI/stdio MCP workflows, known/missing companion inputs and shipped Joplin controls. Preserve reproducible scripts, source pins and compact correctness/resource/token records without archiving applications. Fixes #3926. Part of #4027. Co-authored-by: Kaoru0822 <208281322+kaoru0822-kitauji@users.noreply.github.com>