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>
