fix(markdown): resolve wikilink same-page anchors and heading fragments

[SomSamantray]

Summary

Obsidian wikilinks [[#Heading]] and [[Page#Heading|alias]] produced no graph edge before this change: the extractor's regex could not match a bare same-page anchor at all, and it discarded the heading fragment on anchored links. Entities referenced only through these forms stayed orphaned in the graph. Same-page anchors now resolve to that heading's node in the same file — resolved after the scan so forward references work, first occurrence wins for duplicated titles, and a heading that does not exist resolves to nothing rather than a dangling edge. Anchored cross-page links resolve to the page's node, matching the anchor-stripping semantics inline links already had, and dedup with their plain [[Page]] form.

Fixes #3333.

Validation: 7 new regression tests in tests/test_languages.py, written failing first (red on the pre-fix regex); full suite 5,241 passed / 0 failed with tests/test_skillgen.py excluded — its checks read git objects pinned at a historical ref that shallow local clones do not carry, and PR CI full-clones and covers them; ruff check clean; an end-to-end extract() run verified anchor edges merge into real nodes (no ghost endpoints).

Session-settled decisions carried from planning: PR process constraints — no Compound Engineering badge, no plan artifacts in the commit, repo contribution guidelines followed (user-directed, over the CE-branded pipeline default).

Unapplied review findings

• P3 — graphify/extractors/markdown.py:433 — Shared linked_targets dedup lets a cross-page link steal a same-page anchor's target when the heading id collides with a file-node id (validated true; validator reproduced the silent one-edge drop)
  • suggested_fix: Use a separate dedup set for same-page anchor targets so a heading-target anchor and a file-target cross-page link can never suppress each other even when their ids coincide under make_id's recipe. Plus a regression test for the collision pair.

Review run context: run_id 20260904-230257-2c5b597a, artifact /tmp/compound-engineering-501/ce-code-review/20260904-230257-2c5b597a.

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Formal verification. 3 change(s) tested, no difference found (not proven).

---

Graphify review — findings

Adds anchored-wikilink support to the Markdown extractor: [[Page#Heading|alias]] now resolves to Page's node (anchor stripped, deduped against a plain [[Page]] link), while a same-page [[#Heading]] resolves to that heading's node in the same file. Same-page anchors are deferred and resolved after the full scan against a first-occurrence-wins heading map, so a link may precede its target; a missing heading, a self-reference, or a degenerate form ([[]], [[#]], [[|alias]]) produces no edge rather than a dangling one.

No blocking issues surfaced. 5 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 590 functions depend on the 590 functions this change touches.

Health — this change adds coupling hotspots:

• new: extract_markdown() — 15 callers, 8 callees

Verification — 590 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: 590 function(s) in the blast radius were not formally verified this run

Formal verification

No difference found (not proven): No behavior difference found in god\_nodes (not a proof).

The verifier ran both versions of god\_nodes on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

Could not verify: Could not verify build\_from\_json.

The verifier did not have enough to check build\_from\_json, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 6 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly NameError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_absolutize\_source\_files\_in.

The verifier did not have enough to check \_absolutize\_source\_files\_in, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_relativize\_source\_files\_in.

The verifier did not have enough to check \_relativize\_source\_files\_in, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `root` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify dispatch\_command.

The verifier did not have enough to check dispatch\_command, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)

No difference found (not proven): No behavior difference found in to\_canvas (not a proof).

The verifier ran both versions of to\_canvas on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

Could not verify: Could not verify to\_obsidian.

The verifier did not have enough to check to\_obsidian, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 2 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify extract.

The verifier did not have enough to check extract, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `cache_root` is annotated `Path | None` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_resolve\_cpp\_member\_calls.

The verifier did not have enough to check \_resolve\_cpp\_member\_calls, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 1 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_resolve\_csharp\_member\_calls.

The verifier did not have enough to check \_resolve\_csharp\_member\_calls, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 1 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_resolve\_java\_member\_calls.

The verifier did not have enough to check \_resolve\_java\_member\_calls, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 1 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_resolve\_swift\_member\_calls.

The verifier did not have enough to check \_resolve\_swift\_member\_calls, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 1 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_extract\_generic.

The verifier did not have enough to check \_extract\_generic, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify extract\_markdown.

The verifier did not have enough to check extract\_markdown, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_resolve\_cross\_file\_imports.

The verifier did not have enough to check \_resolve\_cross\_file\_imports, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: the input domain has 81 values but only 9 distinct were tested — a small finite domain must be EXHAUSTED, not sampled (an untested input could invert the result)

Could not verify: Could not verify global\_add.

The verifier did not have enough to check global\_add, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `source_path` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify save\_query\_result.

The verifier did not have enough to check save\_query\_result, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `memory_dir` is annotated `Path` — outside the synthesizable primitive/collection set

Could not verify: Could not verify \_copy\_skill\_file.

The verifier did not have enough to check \_copy\_skill\_file, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly KeyError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify vscode\_install.

The verifier did not have enough to check vscode\_install, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 29 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly NameError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_parse\_cargo.

The verifier did not have enough to check \_parse\_cargo, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 2 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_parse\_pyproject.

The verifier did not have enough to check \_parse\_pyproject, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: non-vacuity: domain too small (only 2 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous

Could not verify: Could not verify \_build\_server.

The verifier did not have enough to check \_build\_server, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous

No difference found (not proven): No behavior difference found in \_node\_search\_text (not a proof).

The verifier ran both versions of \_node\_search\_text on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.

Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.

Note: An input the sampler did not try could still differ.

Could not verify: Could not verify \_score\_query.

The verifier did not have enough to check \_score\_query, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: not verifiable: all 45 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly TypeError — names the real obstacle, not a sampling gap)

Could not verify: Could not verify \_rebase\_relative\_source\_files.

The verifier did not have enough to check \_rebase\_relative\_source\_files, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `source_root` is annotated `Path` — outside the synthesizable primitive/collection set

· 1 more finding(s) on lines outside this diff (see the check run).