fix(query): reach the not-indexed marker on the not_found path

query_graph returns early with status not_found for every pattern except
consumers_of and file_summary, so an unresolved target never reached the
empty-result path where the confidence marker is attached. The marker was
only observable through file_summary, which is what the original test used.

Attach it to the not_found response too, and check for an empty or stale
graph before declaring a target simply unindexed. A stale graph explains
the miss and has a remedy, so it outranks wording that reads like a
permanent parser limitation. Verified against this repository's own graph,
built three months and many commits behind HEAD: callers_of on a function
that plainly exists now says the graph predates HEAD and to update it,
where before it said the symbol was not indexed.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012fHfGDiZedoxjpKzanHri3