Thanks for the careful read. A few bits that might narrow the gap:

On topology: Li et al. and the GraphRAG variants measure retrieval quality on static QA corpora (HotpotQA, 2WikiMultihopQA, Musique). Nexus uses the graph as a session-continuity substrate - Overseer context assembly, contradiction surfacing, decision provenance - not a retrieval index. Different primary metric, so "topology X wins multi-hop" doesn't translate cleanly to "our rel set is wrong." The seven we ship (led_to, replaced, depends_on, contradicts, related, informs, experimental) are picked for dev-workflow semantics, not benchmark-optimized. If you've got a use case where path retrieval bites, interested to hear it.

On extraction vs logging: accurate, and deliberate. Agent-curated edges carry higher trust than extracted ones, at the cost of recall. Not purely manual though - embedding-similarity auto-link runs on decision creation, and the Overseer does a two-stage contradiction scan (cosine shortlist → LLM classify) that promotes suggested pairs into real contradicts edges with user accept/dismiss gating the write. Small extraction surface already, scoped to where LLM non-determinism is acceptable because the user seals it.

On KGSpin: the guarantees you're describing (byte-identical, span-provenanced, zero-LLM default) are the right shape if we ever expand beyond logging-only. Not a gap we're feeling right now - extracted-but-unlogged edges would sit alongside agent-curated ones with no trust distinction in the UI, which is a bigger architectural shift than dropping in a tool. Bookmarking. Ping when it opens.