graphify update regeneration: semantic hashes now populated in
manifest.json, graph rebuilt (1634 nodes, 3179 edges). Track the map
(5 curated files + .graphify_root) so a fresh checkout starts with it;
cost.json, cache/, dated snapshots and .rebuild.lock stay ignored.
AGENTS.md: drop stale Relevant skills and Notes sections; graphify rule
now says to always query the graph first.
sulthan