fix(parse-knowledge-base): extract CommonMark [](page.md) links in Karpathy code path (#361)

[tirth8205]

Summary

Closes #361.

/understand-knowledge's deterministic parser extracted links only via [[wikilink]] syntax. A Karpathy-pattern wiki (has index.md + multiple cross-linked .md files + schema) that uses CommonMark [label](page.md) links — common on GitHub/GitLab where [[wikilinks]] aren't rendered — was detected as karpathy but produced zero deterministic edges. The graph then had to be inferred entirely from prose by the LLM phase, producing a noisy, unreliable result instead of the real link structure.

This PR extracts [label](page.md) links inside the existing Karpathy code path, alongside the existing [[ ]] handling. Both parse_index (for ## Section → article category membership) and the per-article extraction loop now scan both link styles, so category membership and inter-article edges are recovered for Karpathy wikis that use CommonMark links — pure or mixed.

Gap vs existing issues

• Improve Karpathy wiki parser compatibility for title-case infra files and repo-root wiki links #342 addresses [[wikilink]] path resolution (title-case Index.md, repo-root prefixes) — still wikilink-only, doesn't extract [](page.md).
• feat(understand-knowledge): detect and parse doctrine-format markdown corpora #312 adds [](path.md) parsing but as a separate doctrine format detected only when index.md is absent, with explicit "Karpathy detection takes precedence." A wiki that has index.md and uses markdown links is therefore still routed to the Karpathy path and still yields 0 edges.

This PR covers the case neither addresses: Karpathy-detected + CommonMark links.

What changed

In understand-anything-plugin/skills/understand-knowledge/parse-knowledge-base.py:

• MD_LINK_RE — CommonMark [label](target) regex with image-link (!) negative lookbehind.
• is_internal_md_target — filters external URLs (http://, mailto:, …), bare anchors (#section), non-.md assets.
• extract_md_links — strips fenced code blocks, then collects internal-md targets.
• build_path_to_stem_map — case-insensitive map from relative posix-path.md → article stem, used for path-based resolution.
• _normalise_md_target — normalises pages/x.md, ./pages/x.md, and /pages/x.md to the same key; strips #fragment and ?query; rejects paths that escape wiki_root via ...
• resolve_md_link — resolves a CommonMark target to article:<stem> against path_map, gated by the known-article-IDs set just like resolve_wikilink.
• parse_index — under each ## Section, also collects CommonMark links into a new md_links: list[str] parallel to articles: list[str] (existing key, unchanged shape).
• parse_wiki — builds md_category_lookup (keyed by resolved article:<id>), threads md-link extraction through the article loop, emits both related and categorized_under edges for md-link targets, and updates stats with a new mdLinks counter.

Backward compatibility

• Pure [[wikilink]] wikis produce identical edges, stats (modulo the new mdLinks: 0 key), and node shapes (verified by ParseWikiPureWikilinkRegressionTests).
• extract_wikilinks is untouched.
• cat["articles"] remains list[str]; cat["md_links"] is additive.
• knowledgeMeta.mdLinks is only emitted when the article has md-links (so existing pure-wikilink manifests stay byte-for-byte equivalent in that field too).
• The stderr report only includes the md-links segment when non-zero.

Test plan

Added tests/skill/understand-knowledge/test_parse_knowledge_base.py — 38 unit tests across 7 classes:

• IsInternalMdTargetTests (6) — accepts relative/absolute/./ md paths, with #anchor or ?query; rejects external URLs, bare anchors, non-md assets.
• ExtractMdLinksTests (7) — basic extraction, skips image links, external URLs, fenced code blocks, anchors, non-md; preserves wikilinks untouched.
• NormaliseMdTargetTests (7) — bare relative, ./ prefix, absolute (/), ../ traversal, escape rejection, query/fragment strip, lowercase normalisation.
• ParseWikiCommonMarkOnlyTests (6) — regression for understand-knowledge: Karpathy wikis using CommonMark [](page.md) links yield 0 deterministic edges #361: pure CommonMark Karpathy wiki produces real edges, categorisation, and category membership counts.
• ParseWikiMixedSyntaxTests (4) — wikis using both [[ ]] and [](page.md) produce edges from both styles in both related and categorized_under.
• ParseWikiPureWikilinkRegressionTests (4) — existing pure-wikilink wikis stay identical (no mdLinks key, same edge set, same category lookups).
• ResolveMdLinkTests (4) — resolve_md_link returns correct article:<id> for relative + absolute; None for unresolved or out-of-set.

End-to-end manual verification:

• Pure CommonMark Karpathy wiki: produces 2 related + 2 categorized_under edges (was 0 pre-fix).
• Pure wikilink Karpathy wiki: produces same 2+2 edges as before (no regression).
• All 38 new tests pass: python3 tests/skill/understand-knowledge/test_parse_knowledge_base.py -v
• All 69 existing tests in tests/skill/understand/test_merge_batch_graphs.py still pass.