sensemaking 0.15.1 → 0.15.3

package/dist/cjs/features/links.js

@@ -55,6 +55,15 @@ function _unsupported_iterable_to_array(o, minLen) {
 // Wikilinks ([[target]], [[target#anchor|alias]], embeds), internal markdown links, and
 // frontmatter values that are exactly a wikilink ("[[X]]"; mid-string and ![[...]] forms are
 // not links there -- Obsidian's rule, probe-verified).
+// One rule for [[inner]] text wherever it appears: alias stripped after |, a leading #
+// keeps the anchor as the target (a same-note self-link needs a heading name), otherwise
+// the anchor splits off. Null = not a link.
+function parseWikilinkInner(inner) {
+    var beforeAlias = inner.split('|')[0].trim();
+    if (beforeAlias.startsWith('#')) return beforeAlias.length > 1 ? beforeAlias : null;
+    var target = beforeAlias.split('#')[0].trim();
+    return target || null;
+}
 function extract(_raw, rawBody, _search, data) {
     var body = /\[\[|\]\(/.test(rawBody) ? (0, _fencests.maskRegions)(rawBody) : rawBody;
     var seen = new Set();
@@ -71,20 +80,12 @@ function extract(_raw, rawBody, _search, data) {
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
         // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still
-        // matches; anchor and alias split off in code, since a class-based regex stops at the ].
+        // matches; anchor and alias split off in parseWikilinkInner.
         for(var _iterator = body.matchAll(/\[\[(.*?)\]\]/g)[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
             var m = _step.value;
             var _m_index;
-            var embed = body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!';
-            // [[#Heading]]: a same-note anchor link, which Obsidian resolves to a self-edge. Keep the
-            // target as written (leading #) so resolveTarget can special-case it.
-            var beforeAlias = m[1].split('|')[0].trim();
-            if (beforeAlias.startsWith('#')) {
-                if (beforeAlias.length > 1) add(beforeAlias, embed);
-                continue;
-            }
-            var target = beforeAlias.split('#')[0].trim();
-            if (target) add(target, embed);
+            var target = parseWikilinkInner(m[1]);
+            if (target) add(target, body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!');
         }
     } catch (err) {
         _didIteratorError = true;
@@ -111,8 +112,10 @@ function extract(_raw, rawBody, _search, data) {
         for(var _iterator1 = body.matchAll(/(!)?\[[^\]]*\]\(((?:[^()\s]|\([^()\s]*\))+)(?:\s+(?:"[^)]*"|'[^)]*'))?\)/g)[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
             var m1 = _step1.value;
             var dest = m1[2].trim();
+            // External: a URI scheme prefix (mailto:, tel:, data:, https:...), protocol-relative
+            // //host, a www. shorthand, or a scheme anywhere (the malformed double-paren case).
             if (!dest || dest.includes('://')) continue;
-            if (/^www\./i.test(dest)) continue;
+            if (/^([a-z][a-z0-9+.-]*:|\/\/|www\.)/i.test(dest)) continue;
             var target1 = dest.startsWith('#') ? dest : dest.split('#')[0];
             if (target1) add(target1, m1[1] === '!');
         }
@@ -143,10 +146,8 @@ function extract(_raw, rawBody, _search, data) {
                     if (typeof item !== 'string') continue;
                     var m2 = /^\[\[(.*)\]\]$/.exec(item.trim());
                     if (!m2) continue;
-                    var inner = m2[1].split('|')[0].trim();
-                    var target2 = inner.split('#')[0].trim();
+                    var target2 = parseWikilinkInner(m2[1]);
                     if (target2) add(target2, false);
-                    else if (inner.startsWith('#') && inner.length > 1) add(inner, false);
                 }
             } catch (err) {
                 _didIteratorError3 = true;

package/dist/cjs/features/links.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/links.ts"],"sourcesContent":["import posix from 'node:path/posix';\nimport type { DatabaseSync } from 'node:sqlite';\nimport { maskRegions } from '../fences.ts';\nimport type { FileStat } from '../scan.ts';\nimport type { Feature, ReconcileDelta } from './types.ts';\n\n// links(src, target, target_base, dst, embed): target as written, target_base its baseKey\n// (indexed, for the incremental resolve below), dst the resolved path or NULL (a\n// queryable dead link), embed whether it's `![[x]]`/`![](x.md)` rather than `[[x]]`/`[](x.md)`\n// -- Obsidian's grain: a target both linked and embedded in the same note is two rows.\n\n// Wikilinks ([[target]], [[target#anchor|alias]], embeds), internal markdown links, and\n// frontmatter values that are exactly a wikilink (\"[[X]]\"; mid-string and ![[...]] forms are\n// not links there -- Obsidian's rule, probe-verified).\nfunction extract(_raw: string, rawBody: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): Array<{ target: string; embed: boolean }> {\n  const body = /\\[\\[|\\]\\(/.test(rawBody) ? maskRegions(rawBody) : rawBody;\n  const seen = new Set<string>();\n  const results: Array<{ target: string; embed: boolean }> = [];\n  const add = (target: string, embed: boolean) => {\n    const key = `${target}\\0${embed ? '1' : '0'}`;\n    if (seen.has(key)) return;\n    seen.add(key);\n    results.push({ target, embed });\n  };\n  // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still\n  // matches; anchor and alias split off in code, since a class-based regex stops at the ].\n  for (const m of body.matchAll(/\\[\\[(.*?)\\]\\]/g)) {\n    const embed = body[(m.index ?? 0) - 1] === '!';\n    // [[#Heading]]: a same-note anchor link, which Obsidian resolves to a self-edge. Keep the\n    // target as written (leading #) so resolveTarget can special-case it.\n    const beforeAlias = m[1].split('|')[0].trim();\n    if (beforeAlias.startsWith('#')) {\n      if (beforeAlias.length > 1) add(beforeAlias, embed);\n      continue;\n    }\n    const target = beforeAlias.split('#')[0].trim();\n    if (target) add(target, embed);\n  }\n  // Any internal destination, not only .md-suffixed: Obsidian gives markdown links full\n  // linkpath resolution, so \\](Zektor) resolves like [[Zektor]] and \\](#anchor) is a\n  // self-edge. External URLs (a scheme anywhere survives the malformed double-paren case)\n  // and titled links (dest stops at whitespace) are skipped.\n  // A space in the destination is only valid ahead of a quoted title; a domain-shaped first\n  // segment (www.example.com/...) is external even without a scheme.\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(((?:[^()\\s]|\\([^()\\s]*\\))+)(?:\\s+(?:\"[^)]*\"|'[^)]*'))?\\)/g)) {\n    const dest = m[2].trim();\n    if (!dest || dest.includes('://')) continue;\n    if (/^www\\./i.test(dest)) continue;\n    const target = dest.startsWith('#') ? dest : dest.split('#')[0];\n    if (target) add(target, m[1] === '!');\n  }\n  for (const value of Object.values(data ?? {})) {\n    for (const item of Array.isArray(value) ? value : [value]) {\n      if (typeof item !== 'string') continue;\n      const m = /^\\[\\[(.*)\\]\\]$/.exec(item.trim());\n      if (!m) continue;\n      const inner = m[1].split('|')[0].trim();\n      const target = inner.split('#')[0].trim();\n      if (target) add(target, false);\n      else if (inner.startsWith('#') && inner.length > 1) add(inner, false);\n    }\n  }\n  return results;\n}\n\nfunction cleanTarget(target: string): string {\n  return target.replace(/\\\\/g, '/').replace(/^\\.\\//, '');\n}\n\nfunction baseKey(path: string): string {\n  return posix.basename(path).replace(/\\.md$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking\n// note's directory, then basename match (shortest path wins on ties -- verified against a\n// cold-loaded Obsidian vault on 6+ real collision pairs; byBase's lists are pre-sorted that way).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.\n  if (target.startsWith('#')) return src;\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  const candidates = byBase.get(baseKey(clean));\n  if (!candidates) return null;\n  // The linking note itself wins a basename collision (Obsidian resolves to self before the\n  // shortest-path rule -- cold-load verified on the hub corpus).\n  return candidates.includes(src) ? src : candidates[0];\n}\n\n// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own\n// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  const paths = files.map((f) => f.relPath).sort((a, b) => a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));\n  for (const path of paths) {\n    const key = baseKey(path);\n    const list = byBase.get(key);\n    if (list) list.push(path);\n    else byBase.set(key, [path]);\n  }\n  return byBase;\n}\n\ninterface LinkRow {\n  src: string;\n  target: string;\n  dst: string | null;\n  embed: number;\n}\n\n// Applies resolveTarget to `rows`, writing only rows whose dst actually changes. The UPDATE\n// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's\n// mismatch rewrites both.\nfunction resolveRows(db: DatabaseSync, rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): boolean {\n  const update = db.prepare('UPDATE links SET dst = ? WHERE src = ? AND target = ?');\n  let changed = false;\n  for (const row of rows) {\n    const dst = resolveTarget(row.src, row.target, pathSet, byBase);\n    if (dst !== row.dst) {\n      update.run(dst, row.src, row.target);\n      changed = true;\n    }\n  }\n  return changed;\n}\n\n// A new or deleted file can change any note's resolution, so re-resolve the whole table.\n// Fallback for cold builds and large deltas -- see afterReconcile's threshold.\nfunction resolveAll(db: DatabaseSync, files: FileStat[]): boolean {\n  const pathSet = new Set(files.map((f) => f.relPath));\n  const byBase = buildByBase(files);\n  const rows = db.prepare('SELECT src, target, dst, embed FROM links').all() as unknown as LinkRow[];\n  return resolveRows(db, rows, pathSet, byBase);\n}\n\n// Re-resolve only what this reconcile could have touched: re-stored sources, links whose\n// target basename matches an added/vanished file, and links whose dst just vanished. All\n// three are indexed lookups, so this never reads the whole table.\nfunction resolveIncremental(db: DatabaseSync, delta: ReconcileDelta): boolean {\n  const pathSet = new Set(delta.files.map((f) => f.relPath));\n  const byBase = buildByBase(delta.files);\n\n  const changedBasenames = new Set<string>();\n  for (const p of delta.added) changedBasenames.add(baseKey(p));\n  for (const p of delta.vanished) changedBasenames.add(baseKey(p));\n\n  // \\0 can't appear in a path or target, so the key never collides; a space can.\n  const candidates = new Map<string, LinkRow>();\n  const collect = (rows: LinkRow[]) => {\n    for (const row of rows) candidates.set(`${row.src}\\0${row.target}\\0${row.embed}`, row);\n  };\n  // Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable\n  // limit (SQLITE_MAX_VARIABLE_NUMBER, 32766).\n  const collectIn = (column: string, keys: string[]) => {\n    for (let i = 0; i < keys.length; i += 500) {\n      const chunk = keys.slice(i, i + 500);\n      const placeholders = chunk.map(() => '?').join(', ');\n      collect(db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${placeholders})`).all(...chunk) as unknown as LinkRow[]);\n    }\n  };\n\n  collectIn('src', delta.reparsed);\n  collectIn('target_base', [...changedBasenames]);\n  collectIn('dst', delta.vanished);\n\n  return resolveRows(db, [...candidates.values()], pathSet, byBase);\n}\n\n// Resolved edges, for rank and for search's graph expansion.\nexport function linkEdges(db: DatabaseSync): [string, string][] {\n  // One edge per row, as 0.12's grain always had it -- two written targets resolving to one\n  // dst stay two edges (a weight the fusion evals were gated on). The only exclusion is an\n  // embed whose exact (src, target) also exists as a link: that second row is new with the\n  // embed grain and would double an edge that used to be one row. The NOT EXISTS probes the\n  // primary key and fires only for embed rows; both branches still scan the table.\n  // Self-edges (same-note anchors) are excluded here so PageRank mass is not self-recycled --\n  // Obsidian's own graph view hides self-loops too. The rows themselves stay in the table for\n  // backlinks/peek.\n  const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0 AND src != dst\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1 AND src != dst\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;\n  return (db.prepare(sql).all() as Array<{ src: string; dst: string }>).map((r) => [r.src, r.dst]);\n}\n\n// remove() has already deleted the rows by the time afterReconcile runs, so it records here\n// whether they carried edges. Keyed on the delta object, so the state dies with the reconcile.\nconst removedWithLinks = new WeakMap<ReconcileDelta, Set<string>>();\n\nfunction recordRemoved(delta: ReconcileDelta, path: string): void {\n  let set = removedWithLinks.get(delta);\n  if (!set) {\n    set = new Set();\n    removedWithLinks.set(delta, set);\n  }\n  set.add(path);\n}\n\n// remove() runs per path; the vanished list is an array, so cache the Set per delta.\nconst vanishedSets = new WeakMap<ReconcileDelta, Set<string>>();\nfunction vanishedSet(delta: ReconcileDelta): Set<string> {\n  let set = vanishedSets.get(delta);\n  if (!set) {\n    set = new Set(delta.vanished);\n    vanishedSets.set(delta, set);\n  }\n  return set;\n}\n\nexport const links: Feature = {\n  name: 'links',\n  schema(db) {\n    db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');\n    db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');\n  },\n  extract,\n  // Reparsed docs are diffed in store() below instead of wiped here: deleting and\n  // re-inserting resets dst to NULL, which made every touch-only reparse read as an edge\n  // change and recompute PageRank -- measured as most of the remaining update cost.\n  remove(db, path, delta) {\n    if (!vanishedSet(delta).has(path)) return;\n    const result = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    if (Number(result.changes) > 0) recordRemoved(delta, path);\n  },\n  store(db, path, extracted, delta) {\n    const targets = extracted as Array<{ target: string; embed: boolean }>;\n    // Stale rows (target/embed pairs the new parse no longer contains) are real edge removals.\n    // \\0 can't appear in a target, so the composite key never collides.\n    let stale: ReturnType<ReturnType<DatabaseSync['prepare']>['run']>;\n    if (targets.length === 0) {\n      stale = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    } else {\n      const placeholders = targets.map(() => '?').join(', ');\n      const keys = targets.map((t) => `${t.target}\\0${t.embed ? '1' : '0'}`);\n      stale = db.prepare(`DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (${placeholders})`).run(path, ...keys);\n    }\n    if (Number(stale.changes) > 0) recordRemoved(delta, path);\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same\n    // value and reports no change; only genuinely new rows start at NULL.\n    const insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base');\n    // A same-note anchor's dst is always its own src, never another file's basename, so it\n    // gets no target_base -- SQL's `IN` never matches NULL, keeping it out of\n    // resolveIncremental's cross-file collectIn('target_base', ...) entirely.\n    for (const { target, embed } of targets) insert.run(path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0);\n  },\n  afterReconcile(db, delta) {\n    // Any deleted rows that carried edges mean the edge set shrank -- whether the file\n    // vanished or was reparsed down to fewer/no links. dstChanged alone misses the\n    // reparsed-to-zero-links case (no surviving rows to re-resolve).\n    const removeHadLinks = (removedWithLinks.get(delta)?.size ?? 0) > 0;\n\n    const churn = delta.reparsed.length + delta.vanished.length;\n    // Past this share of the tree, a full pass is the only one guaranteed to match\n    // resolveTarget's ambiguity rules. A cold build clears the threshold on its own.\n    const large = delta.files.length === 0 || churn > 0.2 * delta.files.length;\n\n    const dstChanged = large ? resolveAll(db, delta.files) : resolveIncremental(db, delta);\n    delta.linksChanged = dstChanged || removeHadLinks;\n  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Null = not a link.\nfunction parseWikilinkInner(inner: string): string | null {\n  const beforeAlias = inner.split('|')[0].trim();\n  if (beforeAlias.startsWith('#')) return beforeAlias.length > 1 ? beforeAlias : null;\n  const target = beforeAlias.split('#')[0].trim();\n  return target || null;\n}\n\nfunction extract(_raw: string, rawBody: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): Array<{ target: string; embed: boolean }> {\n  const body = /\\[\\[|\\]\\(/.test(rawBody) ? maskRegions(rawBody) : rawBody;\n  const seen = new Set<string>();\n  const results: Array<{ target: string; embed: boolean }> = [];\n  const add = (target: string, embed: boolean) => {\n    const key = `${target}\\0${embed ? '1' : '0'}`;\n    if (seen.has(key)) return;\n    seen.add(key);\n    results.push({ target, embed });\n  };\n  // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still\n  // matches; anchor and alias split off in parseWikilinkInner.\n  for (const m of body.matchAll(/\\[\\[(.*?)\\]\\]/g)) {\n    const target = parseWikilinkInner(m[1]);\n    if (target) add(target, body[(m.index ?? 0) - 1] === '!');\n  }\n  // Any internal destination, not only .md-suffixed: Obsidian gives markdown links full\n  // linkpath resolution, so \\](Zektor) resolves like [[Zektor]] and \\](#anchor) is a\n  // self-edge. External URLs (a scheme anywhere survives the malformed double-paren case)\n  // and titled links (dest stops at whitespace) are skipped.\n  // A space in the destination is only valid ahead of a quoted title; a domain-shaped first\n  // segment (www.example.com/...) is external even without a scheme.\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(((?:[^()\\s]|\\([^()\\s]*\\))+)(?:\\s+(?:\"[^)]*\"|'[^)]*'))?\\)/g)) {\n    const dest = m[2].trim();\n    // External: a URI scheme prefix (mailto:, tel:, data:, https:...), protocol-relative\n    // //host, a www. shorthand, or a scheme anywhere (the malformed double-paren case).\n    if (!dest || dest.includes('://')) continue;\n    if (/^([a-z][a-z0-9+.-]*:|\\/\\/|www\\.)/i.test(dest)) continue;\n    const target = dest.startsWith('#') ? dest : dest.split('#')[0];\n    if (target) add(target, m[1] === '!');\n  }\n  for (const value of Object.values(data ?? {})) {\n    for (const item of Array.isArray(value) ? value : [value]) {\n      if (typeof item !== 'string') continue;\n      const m = /^\\[\\[(.*)\\]\\]$/.exec(item.trim());\n      if (!m) continue;\n      const target = parseWikilinkInner(m[1]);\n      if (target) add(target, false);\n    }\n  }\n  return results;\n}\n\nfunction cleanTarget(target: string): string {\n  return target.replace(/\\\\/g, '/').replace(/^\\.\\//, '');\n}\n\nfunction baseKey(path: string): string {\n  return posix.basename(path).replace(/\\.md$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking\n// note's directory, then basename match (shortest path wins on ties -- verified against a\n// cold-loaded Obsidian vault on 6+ real collision pairs; byBase's lists are pre-sorted that way).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.\n  if (target.startsWith('#')) return src;\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  const candidates = byBase.get(baseKey(clean));\n  if (!candidates) return null;\n  // The linking note itself wins a basename collision (Obsidian resolves to self before the\n  // shortest-path rule -- cold-load verified on the hub corpus).\n  return candidates.includes(src) ? src : candidates[0];\n}\n\n// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own\n// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  const paths = files.map((f) => f.relPath).sort((a, b) => a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));\n  for (const path of paths) {\n    const key = baseKey(path);\n    const list = byBase.get(key);\n    if (list) list.push(path);\n    else byBase.set(key, [path]);\n  }\n  return byBase;\n}\n\ninterface LinkRow {\n  src: string;\n  target: string;\n  dst: string | null;\n  embed: number;\n}\n\n// Applies resolveTarget to `rows`, writing only rows whose dst actually changes. The UPDATE\n// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's\n// mismatch rewrites both.\nfunction resolveRows(db: DatabaseSync, rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): boolean {\n  const update = db.prepare('UPDATE links SET dst = ? WHERE src = ? AND target = ?');\n  let changed = false;\n  for (const row of rows) {\n    const dst = resolveTarget(row.src, row.target, pathSet, byBase);\n    if (dst !== row.dst) {\n      update.run(dst, row.src, row.target);\n      changed = true;\n    }\n  }\n  return changed;\n}\n\n// A new or deleted file can change any note's resolution, so re-resolve the whole table.\n// Fallback for cold builds and large deltas -- see afterReconcile's threshold.\nfunction resolveAll(db: DatabaseSync, files: FileStat[]): boolean {\n  const pathSet = new Set(files.map((f) => f.relPath));\n  const byBase = buildByBase(files);\n  const rows = db.prepare('SELECT src, target, dst, embed FROM links').all() as unknown as LinkRow[];\n  return resolveRows(db, rows, pathSet, byBase);\n}\n\n// Re-resolve only what this reconcile could have touched: re-stored sources, links whose\n// target basename matches an added/vanished file, and links whose dst just vanished. All\n// three are indexed lookups, so this never reads the whole table.\nfunction resolveIncremental(db: DatabaseSync, delta: ReconcileDelta): boolean {\n  const pathSet = new Set(delta.files.map((f) => f.relPath));\n  const byBase = buildByBase(delta.files);\n\n  const changedBasenames = new Set<string>();\n  for (const p of delta.added) changedBasenames.add(baseKey(p));\n  for (const p of delta.vanished) changedBasenames.add(baseKey(p));\n\n  // \\0 can't appear in a path or target, so the key never collides; a space can.\n  const candidates = new Map<string, LinkRow>();\n  const collect = (rows: LinkRow[]) => {\n    for (const row of rows) candidates.set(`${row.src}\\0${row.target}\\0${row.embed}`, row);\n  };\n  // Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable\n  // limit (SQLITE_MAX_VARIABLE_NUMBER, 32766).\n  const collectIn = (column: string, keys: string[]) => {\n    for (let i = 0; i < keys.length; i += 500) {\n      const chunk = keys.slice(i, i + 500);\n      const placeholders = chunk.map(() => '?').join(', ');\n      collect(db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${placeholders})`).all(...chunk) as unknown as LinkRow[]);\n    }\n  };\n\n  collectIn('src', delta.reparsed);\n  collectIn('target_base', [...changedBasenames]);\n  collectIn('dst', delta.vanished);\n\n  return resolveRows(db, [...candidates.values()], pathSet, byBase);\n}\n\n// Resolved edges, for rank and for search's graph expansion.\nexport function linkEdges(db: DatabaseSync): [string, string][] {\n  // One edge per row, as 0.12's grain always had it -- two written targets resolving to one\n  // dst stay two edges (a weight the fusion evals were gated on). The only exclusion is an\n  // embed whose exact (src, target) also exists as a link: that second row is new with the\n  // embed grain and would double an edge that used to be one row. The NOT EXISTS probes the\n  // primary key and fires only for embed rows; both branches still scan the table.\n  // Self-edges (same-note anchors) are excluded here so PageRank mass is not self-recycled --\n  // Obsidian's own graph view hides self-loops too. The rows themselves stay in the table for\n  // backlinks/peek.\n  const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0 AND src != dst\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1 AND src != dst\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;\n  return (db.prepare(sql).all() as Array<{ src: string; dst: string }>).map((r) => [r.src, r.dst]);\n}\n\n// remove() has already deleted the rows by the time afterReconcile runs, so it records here\n// whether they carried edges. Keyed on the delta object, so the state dies with the reconcile.\nconst removedWithLinks = new WeakMap<ReconcileDelta, Set<string>>();\n\nfunction recordRemoved(delta: ReconcileDelta, path: string): void {\n  let set = removedWithLinks.get(delta);\n  if (!set) {\n    set = new Set();\n    removedWithLinks.set(delta, set);\n  }\n  set.add(path);\n}\n\n// remove() runs per path; the vanished list is an array, so cache the Set per delta.\nconst vanishedSets = new WeakMap<ReconcileDelta, Set<string>>();\nfunction vanishedSet(delta: ReconcileDelta): Set<string> {\n  let set = vanishedSets.get(delta);\n  if (!set) {\n    set = new Set(delta.vanished);\n    vanishedSets.set(delta, set);\n  }\n  return set;\n}\n\nexport const links: Feature = {\n  name: 'links',\n  schema(db) {\n    db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');\n    db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');\n  },\n  extract,\n  // Reparsed docs are diffed in store() below instead of wiped here: deleting and\n  // re-inserting resets dst to NULL, which made every touch-only reparse read as an edge\n  // change and recompute PageRank -- measured as most of the remaining update cost.\n  remove(db, path, delta) {\n    if (!vanishedSet(delta).has(path)) return;\n    const result = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    if (Number(result.changes) > 0) recordRemoved(delta, path);\n  },\n  store(db, path, extracted, delta) {\n    const targets = extracted as Array<{ target: string; embed: boolean }>;\n    // Stale rows (target/embed pairs the new parse no longer contains) are real edge removals.\n    // \\0 can't appear in a target, so the composite key never collides.\n    let stale: ReturnType<ReturnType<DatabaseSync['prepare']>['run']>;\n    if (targets.length === 0) {\n      stale = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    } else {\n      const placeholders = targets.map(() => '?').join(', ');\n      const keys = targets.map((t) => `${t.target}\\0${t.embed ? '1' : '0'}`);\n      stale = db.prepare(`DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (${placeholders})`).run(path, ...keys);\n    }\n    if (Number(stale.changes) > 0) recordRemoved(delta, path);\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same\n    // value and reports no change; only genuinely new rows start at NULL.\n    const insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base');\n    // A same-note anchor's dst is always its own src, never another file's basename, so it\n    // gets no target_base -- SQL's `IN` never matches NULL, keeping it out of\n    // resolveIncremental's cross-file collectIn('target_base', ...) entirely.\n    for (const { target, embed } of targets) insert.run(path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0);\n  },\n  afterReconcile(db, delta) {\n    // Any deleted rows that carried edges mean the edge set shrank -- whether the file\n    // vanished or was reparsed down to fewer/no links. dstChanged alone misses the\n    // reparsed-to-zero-links case (no surviving rows to re-resolve).\n    const removeHadLinks = (removedWithLinks.get(delta)?.size ?? 0) > 0;\n\n    const churn = delta.reparsed.length + delta.vanished.length;\n    // Past this share of the tree, a full pass is the only one guaranteed to match\n    // resolveTarget's ambiguity rules. 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package/dist/cjs/features/tags.js

@@ -45,83 +45,6 @@ var HTML_TAG_RE = /<\/?[a-zA-Z][^>]*>/g; // tag-shaped only: a comparison's `< 5
 var INLINE_TAG_RE = 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"gu");
 // A markdown link destination `](...)` -- `[text](#anchor)` is a same-page link, not a tag.
 var LINK_DEST_RE = /\]\((?:[^()]|\([^()]*\))*\)/g; // one paren-nesting level, as CommonMark destinations allow: (https://x/a_(b)#frag)
-// CommonMark's HTML-block type-6 list (fixed by the spec, not a drifting enumeration): a line
-// starting with an open or close tag of one of these, at column 0, opens a block that swallows
-// following lines -- including any #tag in them -- until a blank line closes it.
-var HTML_BLOCK_TAGS = new Set([
-    'address',
-    'article',
-    'aside',
-    'base',
-    'basefont',
-    'blockquote',
-    'body',
-    'caption',
-    'center',
-    'col',
-    'colgroup',
-    'dd',
-    'details',
-    'dialog',
-    'dir',
-    'div',
-    'dl',
-    'dt',
-    'fieldset',
-    'figcaption',
-    'figure',
-    'footer',
-    'form',
-    'frame',
-    'frameset',
-    'h1',
-    'h2',
-    'h3',
-    'h4',
-    'h5',
-    'h6',
-    'head',
-    'header',
-    'hr',
-    'html',
-    'iframe',
-    'legend',
-    'li',
-    'link',
-    'main',
-    'menu',
-    'menuitem',
-    'nav',
-    'noframes',
-    'ol',
-    'optgroup',
-    'option',
-    'p',
-    'param',
-    'search',
-    'section',
-    'summary',
-    'table',
-    'tbody',
-    'td',
-    'tfoot',
-    'th',
-    'thead',
-    'title',
-    'tr',
-    'track',
-    'ul'
-]);
-// Type-1 blocks (script/pre/style/textarea): closes on the line holding the matching end tag,
-// not on a blank line, and that line is the last one skipped.
-var HTML_PRE_TAGS = new Set([
-    'script',
-    'pre',
-    'style',
-    'textarea'
-]);
-// An opening or closing tag at column 0, tag name captured for the lookups above.
-var HTML_BLOCK_OPEN_RE = /^<\/?([a-zA-Z][a-zA-Z0-9]*)(?:[ \t]|\/?>|$)/;
 // Strips a leading # (frontmatter entries may carry one) and a trailing /; rejects an
 // all-digit result -- a tag needs at least one non-digit character.
 function normalizeTag(raw) {
@@ -162,59 +85,16 @@ function frontmatterTags(data) {
     return found;
 }
 // #tag tokens outside fenced code blocks, inline code spans, wikilinks, HTML tags, HTML blocks,
-// <!-- --> comments, and link destinations.
+// <!-- --> comments, and link destinations. maskRegions() handles all of those region-level
+// concerns (and code spans, masked once there); this loop only does per-line tag extraction.
 function inlineTags(body) {
     var found = [];
-    var fence = (0, _fencests.fenceTracker)();
-    var comment = (0, _fencests.commentTracker)();
-    var inHtmlBlock = false;
-    var htmlBlockClose = null; // set while inside a type-1 (script/pre/style/textarea) block
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
-        for(var _iterator = body.split('\n')[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
+        for(var _iterator = (0, _fencests.maskRegions)(body).split('\n')[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
             var line = _step.value;
-            if (inHtmlBlock) {
-                // A fence-like line here is still HTML-block content -- the block wins until it closes.
-                if (htmlBlockClose) {
-                    if (htmlBlockClose.test(line)) {
-                        inHtmlBlock = false;
-                        htmlBlockClose = null;
-                    }
-                } else if (/^[ \t>]*$/.test(line)) {
-                    inHtmlBlock = false;
-                }
-                continue;
-            }
-            if (!comment.inComment) {
-                if (fence.feed(line)) continue;
-                if (fence.inFence) continue;
-            }
-            // Obsidian parses nothing inside a <!-- --> comment; mask its span (which may open, close,
-            // or run the whole line) before any other check sees this line's text. Skipped when there
-            // is no comment marker anywhere near this line -- most lines, so worth the branch.
-            var masked = comment.inComment || line.includes('<!--') ? comment.mask(line) : line;
-            // Indented or blockquoted HTML blocks still swallow their content in Obsidian, so the
-            // opener test runs after stripping leading whitespace and > markers.
-            var stripped = masked.replace(/^[ \t>]*/, '');
-            if (stripped[0] === '<') {
-                var openMatch = HTML_BLOCK_OPEN_RE.exec(stripped);
-                if (openMatch) {
-                    var tagName = openMatch[1].toLowerCase();
-                    var isClosingTag = stripped[1] === '/';
-                    if (!isClosingTag && HTML_PRE_TAGS.has(tagName)) {
-                        inHtmlBlock = true;
-                        // Any of the four type-1 closers ends the block, not only the tag that opened it.
-                        htmlBlockClose = /<\/(?:script|pre|style|textarea)>/i;
-                        continue;
-                    }
-                    if (HTML_BLOCK_TAGS.has(tagName)) {
-                        inHtmlBlock = true;
-                        continue;
-                    }
-                }
-            }
-            if (!masked.includes('#')) continue; // most lines; skip the regex work
-            var cleaned = masked.includes('`') ? (0, _fencests.maskCodeSpans)(masked) : masked;
+            if (!line.includes('#')) continue; // most lines; skip the regex work
+            var cleaned = line;
             if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, function(m) {
                 return ' '.repeat(m.length);
             });

package/dist/cjs/features/tags.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/tags.ts"],"sourcesContent":["import { commentTracker, fenceTracker, maskCodeSpans } from '../fences.ts';\nimport type { Feature } from './types.ts';\n\n// tags(path, tag): Obsidian's file.tags grain -- frontmatter list/string tags plus inline\n// #tags from the prose, deduplicated, source not distinguished. 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Null members and non-string\n// members are skipped rather than throwing -- `tags:\\n  -` parses to [null].\nfunction frontmatterTags(data?: Record<string, unknown>): string[] {\n  const raw = data?.tags;\n  const list = Array.isArray(raw) ? raw : typeof raw === 'string' ? 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[raw] : [];\n  const found: string[] = [];\n  for (const item of list) {\n    if (typeof item !== 'string') continue;\n    const tag = normalizeTag(item);\n    if (tag) found.push(tag);\n  }\n  return found;\n}\n\n// #tag tokens outside fenced code blocks, inline code spans, wikilinks, HTML tags, HTML blocks,\n// <!-- --> comments, and link destinations. maskRegions() handles all of those region-level\n// concerns (and code spans, masked once there); this loop only does per-line tag extraction.\nfunction inlineTags(body: string): string[] {\n  const found: string[] = [];\n  for (const line of maskRegions(body).split('\\n')) {\n    if (!line.includes('#')) continue; // most lines; skip the regex work\n    let cleaned = line;\n    if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('](')) cleaned = cleaned.replace(LINK_DEST_RE, (m) => ' '.repeat(m.length));\n    if (cleaned.includes('<')) cleaned = cleaned.replace(HTML_TAG_RE, (m) => ' '.repeat(m.length));\n    for (const m of cleaned.matchAll(INLINE_TAG_RE)) {\n      const tag = normalizeTag(m[1]);\n      if (tag) found.push(tag);\n    }\n  }\n  return found;\n}\n\nfunction extract(_raw: string, body: string, _search?: { title: string; summary: string }, data?: Record<string, unknown>): string[] {\n  return [...new Set([...frontmatterTags(data), ...inlineTags(body)])].sort();\n}\n\nexport const tags: Feature = {\n  name: 'tags',\n  schema(db) {\n    db.exec('CREATE TABLE IF NOT EXISTS tags (\"path\" TEXT, tag TEXT, PRIMARY KEY (\"path\", tag))');\n    db.exec('CREATE INDEX IF NOT EXISTS tags_tag ON tags(tag)');\n  },\n  extract,\n  // Per-file rows with nothing else to resolve, so only a vanished file needs a delete here;\n  // store() below handles a reparse's stale rows itself.\n  remove(db, path, delta) {\n    if (!delta.vanished.includes(path)) return;\n    db.prepare('DELETE FROM tags WHERE \"path\" = ?').run(path);\n  },\n  store(db, path, extracted) {\n    const found = extracted as string[];\n    if (found.length === 0) {\n      db.prepare('DELETE FROM tags WHERE \"path\" = ?').run(path);\n    } else {\n      const placeholders = found.map(() => '?').join(', ');\n      db.prepare(`DELETE FROM tags WHERE \"path\" = ? 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package/dist/cjs/fences.d.cts

@@ -5,6 +5,7 @@ export interface FenceTracker {
 export declare function fenceTracker(): FenceTracker;
 export interface CommentTracker {
     mask(line: string): string;
+    close(): void;
     readonly inComment: boolean;
 }
 export declare function commentTracker(): CommentTracker;

package/dist/cjs/fences.d.ts

@@ -5,6 +5,7 @@ export interface FenceTracker {
 export declare function fenceTracker(): FenceTracker;
 export interface CommentTracker {
     mask(line: string): string;
+    close(): void;
     readonly inComment: boolean;
 }
 export declare function commentTracker(): CommentTracker;

package/dist/cjs/fences.js

@@ -96,21 +96,146 @@ function commentTracker() {
             }
             return out;
         },
+        close: function close() {
+            inComment = false;
+        },
         get inComment () {
             return inComment;
         }
     };
 }
+// CommonMark's HTML-block type-6 list (fixed by the spec, not a drifting enumeration): a line
+// starting with an open or close tag of one of these, at column 0 (leading whitespace/`>`
+// blockquote markers tolerated), opens a block that swallows following lines -- tags, links,
+// and comments alike -- until a blank line closes it.
+var HTML_BLOCK_TAGS = new Set([
+    'address',
+    'article',
+    'aside',
+    'base',
+    'basefont',
+    'blockquote',
+    'body',
+    'caption',
+    'center',
+    'col',
+    'colgroup',
+    'dd',
+    'details',
+    'dialog',
+    'dir',
+    'div',
+    'dl',
+    'dt',
+    'fieldset',
+    'figcaption',
+    'figure',
+    'footer',
+    'form',
+    'frame',
+    'frameset',
+    'h1',
+    'h2',
+    'h3',
+    'h4',
+    'h5',
+    'h6',
+    'head',
+    'header',
+    'hr',
+    'html',
+    'iframe',
+    'legend',
+    'li',
+    'link',
+    'main',
+    'menu',
+    'menuitem',
+    'nav',
+    'noframes',
+    'ol',
+    'optgroup',
+    'option',
+    'p',
+    'param',
+    'search',
+    'section',
+    'summary',
+    'table',
+    'tbody',
+    'td',
+    'tfoot',
+    'th',
+    'thead',
+    'title',
+    'tr',
+    'track',
+    'ul'
+]);
+// Type-1 blocks (script/pre/style/textarea): closes on the line holding the matching end tag,
+// not on a blank line, and that line is the last one swallowed.
+var HTML_PRE_TAGS = new Set([
+    'script',
+    'pre',
+    'style',
+    'textarea'
+]);
+var HTML_PRE_CLOSE_RE = /<\/(?:script|pre|style|textarea)>/i; // any of the four closers ends the block, not only the tag that opened it
+// An opening or closing tag at column 0, tag name captured for the lookups above.
+var HTML_BLOCK_OPEN_RE = /^<\/?([a-zA-Z][a-zA-Z0-9]*)(?:[ \t]|\/?>|$)/;
+var BLANK_LINE_RE = /^[ \t>]*$/; // whitespace/blockquote-markers only -- a paragraph break, and what ends a type-6 block
 function maskRegions(body) {
-    if (!/[`~]/.test(body) && !body.includes('<!--')) return body;
+    if (!/[`~<]/.test(body)) return body;
     var fence = fenceTracker();
     var comment = commentTracker();
+    var inHtmlBlock = false;
+    var htmlBlockClose = null; // set while inside a type-1 (script/pre/style/textarea) block
     return body.split('\n').map(function(line) {
+        if (inHtmlBlock) {
+            if (htmlBlockClose) {
+                if (htmlBlockClose.test(line)) {
+                    inHtmlBlock = false;
+                    htmlBlockClose = null;
+                }
+                return ' '.repeat(line.length);
+            }
+            if (BLANK_LINE_RE.test(line)) {
+                // Block content never feeds the comment tracker, so an inner <!-- was only ever
+                // masked text; nothing to close here.
+                inHtmlBlock = false;
+                return line;
+            }
+            return ' '.repeat(line.length);
+        }
         if (!comment.inComment) {
             var isDelim = fence.feed(line);
             if (isDelim || fence.inFence) return ' '.repeat(line.length);
         }
-        var uncommented = comment.mask(line);
+        var uncommented = comment.inComment || line.includes('<!--') ? comment.mask(line) : line;
+        if (comment.inComment && BLANK_LINE_RE.test(line)) comment.close(); // paragraph-level: dies at the next blank line
+        // Indented or blockquoted HTML blocks still swallow their content in Obsidian, so the
+        // opener test runs after stripping leading whitespace and > markers.
+        var stripped = uncommented.replace(/^[ \t>]*/, '');
+        if (stripped[0] === '<') {
+            var openMatch = HTML_BLOCK_OPEN_RE.exec(stripped);
+            if (openMatch) {
+                var tagName = openMatch[1].toLowerCase();
+                var isClosingTag = stripped[1] === '/';
+                if (!isClosingTag && HTML_PRE_TAGS.has(tagName)) {
+                    // The end condition can be met on the opening line itself: <script>x</script>
+                    // is a one-line block and the next line parses (Obsidian-verified).
+                    if (!HTML_PRE_CLOSE_RE.test(stripped.slice(openMatch[0].length))) {
+                        inHtmlBlock = true;
+                        htmlBlockClose = HTML_PRE_CLOSE_RE;
+                    }
+                    return ' '.repeat(line.length);
+                }
+                if (HTML_BLOCK_TAGS.has(tagName)) {
+                    inHtmlBlock = true;
+                    return ' '.repeat(line.length);
+                }
+            }
+        }
         // Inline code spans hide their content too: `[[x]]` in prose is not a link.
         return uncommented.includes('`') ? maskCodeSpans(uncommented) : uncommented;
     }).join('\n');