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When two edges connect the same (source, target) pair with different relations, the simple-graph collapse was last-write-wins by alphabetical relation, so a specific `calls` was systematically overwritten by a generic `references`/ `uses` — and `references` is not in the callflow filter, so those call sites dropped out of the call graph. A generic relation can no longer clobber a stored non-generic one; the outcome is now order-independent and the edge count is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>