fix(skill): complete induced subgraph in query fallback

[nothariharan]

Summary

Fixes #4314.

The inline NetworkX fallback for /graphify query recorded an edge only when BFS/DFS discovered an unvisited neighbour, so an edge between two already-visited nodes (two seeds, a triangle chord, a cycle arc, a cross-link) was dropped. The fallback returned a traversal tree rather than the induced subgraph over the node set it reports.

graphify query had the identical defect and already fixed it in #2323 via graphify.serve._complete_induced_edges; the inline fallback now mirrors that completion.

Reproduced on v8 with the issue's example (seeds A/B/C; edges A→B, B→C, A→C):

case	before	after
BFS, three seeds	0 edges	3 edges
DFS, three seeds	2 edges (missing B→C)	3 edges
BFS, single seed	2 edges (missing B→C)	3 edges

Changes

• tools/skillgen/fragments/references/query/default.md, tools/skillgen/fragments/core/aider.md, tools/skillgen/fragments/core/devin.md: add an induced-edge completion pass after the BFS/DFS walk. The visited set controls expansion only; edges are completed over the visited set (ordered-pair keys when directed, unordered frozenset otherwise; self-loops skipped; duplicates collapsed; edges incident to unvisited nodes excluded).
• tools/skillgen/gen.py: _is_query_induced_edges_fix_line plus registration in _SANCTIONED_MONOLITH_DIFFS (the monolith round-trip guard).
• Regenerated all 14 graphify/skills/*/references/query.md, graphify/skill-aider.md, graphify/skill-devin.md, and every matching tools/skillgen/expected/* snapshot.
• tests/test_skill_query_fallback_induced_edges.py: extracts the shipped fallback and executes it against a real graphify-out/graph.json; covers seeded nodes, BFS/DFS cross-links, cycles, edge direction, and parallel-edge de-duplication (24 tests across the reference fragment and the shipped aider/devin/codex artifacts).

Verification

• python -m tools.skillgen --check → OK (134 artifacts)
• python -m tools.skillgen --monolith-roundtrip → OK
• python -m tools.skillgen --audit-coverage → OK
• pytest tests/test_skill_query_fallback_induced_edges.py → 24 passed
• Falsified against pre-fix HEAD: the seeded case emits 0 edges before, 3 after; the new fixture also asserts the completion line is present, so a revert fails rather than silently passing.
• Swept the tree: all 35 shipped copies of the fallback now contain the completion; none remain buggy. path uses nx.shortest_path and explain is a one-hop listing, so neither needed changes.

Note: tests/test_skillgen.py::test_no_version_or_timestamp_in_output and tests/test_skill_persisted_scan_options.py fail identically on pristine v8 in an uninstalled source checkout (__version__ == "unknown" / import graphify from a temp cwd). They are unrelated to this change.

Out of scope, same defect class

graphify/benchmark.py::_query_subgraph_tokens records edges the same discovery-coupled way. It only feeds an internal token estimate for graphify benchmark, so it is not part of the /graphify query answer path; flagged for awareness rather than changed here.

Notes for maintainers

• Target branch is v8 (repo default).
• No API or graph-format changes. Output changes only in that previously-omitted edges between visited nodes are now emitted.

[github-actions]

Thanks for the pull request, @nothariharan. A maintainer will review it soon.

Want to talk it through while it is in review? Come join us on our Discord server. For longer-form discussion there is also GitHub Discussions.

A couple of things that speed up review: make sure the test suite passes on Python 3.10 and 3.13, and that the change keeps extraction deterministic.

[graphify-labs]

Graphify reviewed this change.

No issues found by static checks — no coupling regressions or blocking issues in the code graph. That is not the same as safe to merge: see what was not checked.

Not checked: tests were not run; no formal proof of the changed code.

---

Graphify review — findings

Fixes the query fallback's subgraph output so it includes every edge between visited nodes. Previously it emitted only the BFS/DFS traversal-tree edges, which dropped seed-to-seed links, triangle chords and cross-links (#4314). After traversal, a completion pass scans edges incident to the subgraph and appends any missing ones, skipping self-loops, deduping (direction-aware on directed graphs) and keeping cost proportional to the subgraph size. The fix ships in every generated skill variant and their skillgen fragments/expected outputs, with new tests covering directed-edge direction and DFS cross-links.

Review partial — this diff was larger than one review pass covers, so later files were not reviewed; some findings may be missing.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 576 functions depend on the 505 functions this change touches.

Health — grade A; 5 existing hotspot(s) in the area this change touches (pre-existing, not introduced here):

• render() — 13 callers, 5 callees (high)
• audit_coverage() — 8 callers, 6 callees (high)
• main() — 3 callers, 11 callees (medium)
• monolith_roundtrip() — 3 callers, 5 callees (medium)
• test_audit_catches_a_dropped_non_allowlisted_heading() — 0 callers, 6 callees (medium)

Verification — 576 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 576 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

368 of 368 test file(s) selected (100%) via static blast radius.

Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.

• tests/test_affected_cli.py — full-run-safety
• tests/test_affected_defines.py — full-run-safety
• tests/test_affected_member_seed.py — full-run-safety
• tests/test_agents_platform.py — full-run-safety
• tests/test_analyze.py — full-run-safety
• tests/test_anthropic_custom_endpoint.py — full-run-safety
• tests/test_antigravity_install.py — full-run-safety
• tests/test_apm_fallback_version.py — full-run-safety
• tests/test_architecture_doc.py — full-run-safety
• tests/test_astro_extraction.py — full-run-safety
• tests/test_astro_import_ids.py — full-run-safety
• tests/test_atomic_canvas_export.py — full-run-safety
• tests/test_atomic_version_stamp.py — full-run-safety
• tests/test_atomic_writes.py — full-run-safety
• tests/test_backend_env_isolation.py — full-run-safety
• tests/test_backend_extras.py — full-run-safety
• tests/test_benchmark.py — full-run-safety
• tests/test_benchmark_raw_graph.py — full-run-safety
• tests/test_blade_extractor.py — full-run-safety
• tests/test_build.py — full-run-safety
• tests/test_build_located_semantic_identity.py — full-run-safety
• tests/test_build_merge_dedup_scope.py — full-run-safety
• tests/test_build_merge_hyperedges_and_prune.py — full-run-safety
• tests/test_build_merge_shrink_guard.py — full-run-safety
• tests/test_builtin_global_type_refs.py — full-run-safety
• tests/test_cache.py — full-run-safety
• tests/test_cache_stale_import_target.py — full-run-safety
• tests/test_callflow_html.py — full-run-safety
• tests/test_cargo_introspect.py — full-run-safety
• tests/test_cargo_missing_manifest.py — full-run-safety
• tests/test_carried_hyperedge_remap.py — full-run-safety
• tests/test_case_sensitive_resolution.py — full-run-safety
• tests/test_charmap_encoding.py — full-run-safety
• tests/test_chunking.py — full-run-safety
• tests/test_cjs_module_extension.py — full-run-safety
• tests/test_claude_cli_backend.py — full-run-safety
• tests/test_claude_md.py — full-run-safety
• tests/test_cli_broken_pipe.py — full-run-safety
• tests/test_cli_export.py — full-run-safety
• tests/test_cli_help.py — full-run-safety
• tests/test_cloud_cta.py — full-run-safety
• tests/test_cluster.py — full-run-safety
• tests/test_cluster_ambiguous_scale.py — full-run-safety
• tests/test_cluster_exclude_hubs.py — full-run-safety
• tests/test_cobol_extractor.py — full-run-safety
• tests/test_codebuddy.py — full-run-safety
• tests/test_community_hub_labels.py — full-run-safety
• tests/test_community_labels_skill.py — full-run-safety
• tests/test_confidence.py — full-run-safety
• tests/test_corrupt_graph_json.py — full-run-safety
• … and 318 more

non-code file(s) changed (graphify/skill-aider.md, graphify/skill-devin.md, graphify/skills/agents/references/query.md, graphify/skills/amp/references/query.md, graphify/skills/claude/references/query.md …) → running the full suite for safety (a code graph can't see config/fixture/data deps)

changed code file(s) with no mapped test (graphify/skill-aider.md, graphify/skill-devin.md, graphify/skills/agents/references/query.md, graphify/skills/amp/references/query.md, graphify/skills/claude/references/query.md …) — a coverage gap or a missing link — running the full suite rather than only the selected tests

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.

Docs that may be stale (advisory)

• docs/superpowers/plans/2026-05-04-incremental-updates-dedup.md § Task 4: Incremental updates — semantic cache + manifest in __main__.py (lines 603-911): references changed symbols _run