graphify

Path-portability fixes so graphify-out/ artifacts are portable across clones and machines, plus a native-backend extraction fix.

Path portability

• Portable manifest.json — the skill runbooks now relativize manifest keys to the scan root, so graphify --update matches cached files after a clone or move instead of re-extracting the whole corpus. (#1417)
• Hyperedge source_file relativized — build_from_json now relativizes graph.hyperedges[] like nodes and edges, so a semantic subagent's absolute path no longer leaks into graph.json. (#1418)
• Report header shows the scan root — the split-skill runbook passed '.' to report.generate; it now passes the real scan path, so GRAPH_REPORT.md no longer titles itself .. (#1419)
• GRAPHIFY_OUT honoured end-to-end — the custom output-dir override was only respected by some readers, so GRAPHIFY_OUT=custom-out graphify extract still wrote to graphify-out/. It's now resolved through a single graphify.paths module across extract, cluster-only, query/affected/benchmark, save-result, uninstall --purge, cache-check, the manifest/transcripts/memory/converted paths, the build_merge/serve/prs defaults, and the detect scan-exclude. Default behaviour is unchanged. (#1423)

Native-backend extraction

• Hyperedges are now requested on the native path — graphify extract --backend <gemini|claude|claude-cli|openai|kimi|…> never produced hyperedges (the prompt's schema showed an empty array and never described them), while the agent/skill path did. The native prompt now matches the skill spec, so both paths yield the same hyperedge behaviour. (#1430)