sensemaking 0.17.1 → 0.18.0

package/dist/esm/features/embed.js.map

@@ -1 +1 @@
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package/dist/esm/features/index.d.ts

@@ -2,6 +2,6 @@ import type { Config } from '../config/index.js';
 import type { Feature } from './types.js';
 export declare const FEATURES: Feature[];
 export declare function activeFeatures(cfg: Config): Feature[];
-export { linkEdges } from './links.js';
+export { LINK_EDGES_SQL, linkEdges, toEdges } from './links.js';
 export type { Section } from './sections.js';
 export type { Feature } from './types.js';

package/dist/esm/features/index.js

@@ -15,4 +15,4 @@ export const FEATURES = [
 export function activeFeatures(cfg) {
     return FEATURES.filter((feature)=>featureEnabled(cfg, feature.name));
 }
-export { linkEdges } from './links.js';
+export { LINK_EDGES_SQL, linkEdges, toEdges } from './links.js';

package/dist/esm/features/index.js.map

@@ -1 +1 @@
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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/index.ts"],"sourcesContent":["import type { Config } from '../config/index.ts';\nimport { featureEnabled } from '../config/index.ts';\nimport { embed } from './embed.ts';\nimport { links } from './links.ts';\nimport { rank } from './rank.ts';\nimport { sections } from './sections.ts';\nimport { tags } from './tags.ts';\nimport type { Feature } from './types.ts';\n\n// Registry order matters: rank reads the links table in afterReconcile.\nexport const FEATURES: Feature[] = [links, sections, tags, rank, embed];\n\nexport function activeFeatures(cfg: Config): Feature[] {\n  return FEATURES.filter((feature) => featureEnabled(cfg, feature.name));\n}\n\nexport { LINK_EDGES_SQL, linkEdges, toEdges } from './links.ts';\nexport type { Section } from './sections.ts';\nexport type { Feature } from './types.ts';\n"],"names":["featureEnabled","embed","links","rank","sections","tags","FEATURES","activeFeatures","cfg","filter","feature","name","LINK_EDGES_SQL","linkEdges","toEdges"],"mappings":"AACA,SAASA,cAAc,QAAQ,qBAAqB;AACpD,SAASC,KAAK,QAAQ,aAAa;AACnC,SAASC,KAAK,QAAQ,aAAa;AACnC,SAASC,IAAI,QAAQ,YAAY;AACjC,SAASC,QAAQ,QAAQ,gBAAgB;AACzC,SAASC,IAAI,QAAQ,YAAY;AAGjC,wEAAwE;AACxE,OAAO,MAAMC,WAAsB;IAACJ;IAAOE;IAAUC;IAAMF;IAAMF;CAAM,CAAC;AAExE,OAAO,SAASM,eAAeC,GAAW;IACxC,OAAOF,SAASG,MAAM,CAAC,CAACC,UAAYV,eAAeQ,KAAKE,QAAQC,IAAI;AACtE;AAEA,SAASC,cAAc,EAAEC,SAAS,EAAEC,OAAO,QAAQ,aAAa"}

package/dist/esm/features/links.d.ts

@@ -1,4 +1,9 @@
-import type { DatabaseSync } from 'node:sqlite';
+import type { Connection } from '../store/types.js';
 import type { Feature } from './types.js';
-export declare function linkEdges(db: DatabaseSync): [string, string][];
+export declare const LINK_EDGES_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)";
+export declare function toEdges(rows: Array<{
+    src: string;
+    dst: string;
+}>): [string, string][];
+export declare function linkEdges(db: Connection): Promise<[string, string][]>;
 export declare const links: Feature;

package/dist/esm/features/links.js

@@ -107,33 +107,54 @@ function buildByBase(files) {
     }
     return byBase;
 }
-// Applies resolveTarget to `rows`, writing only rows whose dst actually changes. The UPDATE
-// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's
-// mismatch rewrites both.
-function resolveRows(db, rows, pathSet, byBase) {
-    const update = db.prepare('UPDATE links SET dst = ? WHERE src = ? AND target = ?');
-    let changed = false;
+// resolveTarget applied to `rows`, returning just the rows whose dst actually changed -- the
+// caller writes those in one runBatch call, keyed on (src, target) so a link/embed sibling
+// pair sharing one resolution rewrites both.
+function resolveRows(rows, pathSet, byBase) {
+    const changed = [];
     for (const row of rows){
         const dst = resolveTarget(row.src, row.target, pathSet, byBase);
-        if (dst !== row.dst) {
-            update.run(dst, row.src, row.target);
-            changed = true;
-        }
+        if (dst !== row.dst) changed.push({
+            ...row,
+            dst
+        });
     }
     return changed;
 }
+async function writeResolved(db, rows) {
+    if (rows.length === 0) return;
+    await db.runBatch('UPDATE links SET dst = ? WHERE src = ? AND target = ?', rows.map((r)=>[
+            r.dst,
+            r.src,
+            r.target
+        ]));
+}
 // A new or deleted file can change any note's resolution, so re-resolve the whole table.
 // Fallback for cold builds and large deltas -- see afterReconcile's threshold.
-function resolveAll(db, files) {
+async function resolveAll(db, files) {
     const pathSet = new Set(files.map((f)=>f.relPath));
     const byBase = buildByBase(files);
-    const rows = db.prepare('SELECT src, target, dst, embed FROM links').all();
-    return resolveRows(db, rows, pathSet, byBase);
+    const stmt = await db.prepare('SELECT src, target, dst, embed FROM links');
+    const rows = await stmt.all();
+    const changed = resolveRows(rows, pathSet, byBase);
+    await writeResolved(db, changed);
+    return changed.length > 0;
+}
+// Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit
+// (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.
+async function selectIn(db, column, keys) {
+    const rows = [];
+    for(let i = 0; i < keys.length; i += 500){
+        const chunk = keys.slice(i, i + 500);
+        const stmt = await db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${chunk.map(()=>'?').join(', ')})`);
+        rows.push(...await stmt.all(...chunk));
+    }
+    return rows;
 }
 // Re-resolve only what this reconcile could have touched: re-stored sources, links whose
 // target basename matches an added/vanished file, and links whose dst just vanished. All
 // three are indexed lookups, so this never reads the whole table.
-function resolveIncremental(db, delta) {
+async function resolveIncremental(db, delta) {
     const pathSet = new Set(delta.files.map((f)=>f.relPath));
     const byBase = buildByBase(delta.files);
     const changedBasenames = new Set();
@@ -144,113 +165,119 @@ function resolveIncremental(db, delta) {
     const collect = (rows)=>{
         for (const row of rows)candidates.set(`${row.src}\0${row.target}\0${row.embed}`, row);
     };
-    // Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable
-    // limit (SQLITE_MAX_VARIABLE_NUMBER, 32766).
-    const collectIn = (column, keys)=>{
-        for(let i = 0; i < keys.length; i += 500){
-            const chunk = keys.slice(i, i + 500);
-            const placeholders = chunk.map(()=>'?').join(', ');
-            collect(db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${placeholders})`).all(...chunk));
-        }
-    };
-    collectIn('src', delta.reparsed);
-    collectIn('target_base', [
+    collect(await selectIn(db, 'src', delta.reparsed));
+    collect(await selectIn(db, 'target_base', [
         ...changedBasenames
-    ]);
-    collectIn('dst', delta.vanished);
-    return resolveRows(db, [
+    ]));
+    collect(await selectIn(db, 'dst', delta.vanished));
+    const changed = resolveRows([
         ...candidates.values()
     ], pathSet, byBase);
+    await writeResolved(db, changed);
+    return changed.length > 0;
 }
-// Resolved edges, for rank and for search's graph expansion.
-export function linkEdges(db) {
-    // One edge per row, as 0.12's grain always had it -- two written targets resolving to one
-    // dst stay two edges (a weight the fusion evals were gated on). The only exclusion is an
-    // embed whose exact (src, target) also exists as a link: that second row is new with the
-    // embed grain and would double an edge that used to be one row. The NOT EXISTS probes the
-    // primary key and fires only for embed rows; both branches still scan the table.
-    // Self-edges (same-note anchors) are excluded here so PageRank mass is not self-recycled --
-    // Obsidian's own graph view hides self-loops too. The rows themselves stay in the table for
-    // backlinks/peek.
-    const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0 AND src != dst
+// One edge per row, as 0.12's grain always had it -- two written targets resolving to one
+// dst stay two edges (a weight the fusion evals were gated on). The only exclusion is an
+// embed whose exact (src, target) also exists as a link: that second row is new with the
+// embed grain and would double an edge that used to be one row. The NOT EXISTS probes the
+// primary key and fires only for embed rows; both branches still scan the table.
+// Self-edges (same-note anchors) are excluded here so PageRank mass is not self-recycled --
+// Obsidian's own graph view hides self-loops too. The rows themselves stay in the table for
+// backlinks/peek. Exported (not just linkEdges below) so commands/signals.ts's async caller,
+// which only has the Store's prepare(), can run the identical statement itself.
+export const LINK_EDGES_SQL = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0 AND src != dst
     UNION ALL
     SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1 AND src != dst
       AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;
-    return db.prepare(sql).all().map((r)=>[
+export function toEdges(rows) {
+    return rows.map((r)=>[
             r.src,
             r.dst
         ]);
 }
-// remove() has already deleted the rows by the time afterReconcile runs, so it records here
-// whether they carried edges. Keyed on the delta object, so the state dies with the reconcile.
-const removedWithLinks = new WeakMap();
-function recordRemoved(delta, path) {
-    let set = removedWithLinks.get(delta);
-    if (!set) {
-        set = new Set();
-        removedWithLinks.set(delta, set);
-    }
-    set.add(path);
-}
-// remove() runs per path; the vanished list is an array, so cache the Set per delta.
-const vanishedSets = new WeakMap();
-function vanishedSet(delta) {
-    let set = vanishedSets.get(delta);
-    if (!set) {
-        set = new Set(delta.vanished);
-        vanishedSets.set(delta, set);
-    }
-    return set;
+// Resolved edges, for rank (inside reconcile's afterReconcile pass).
+export async function linkEdges(db) {
+    const stmt = await db.prepare(LINK_EDGES_SQL);
+    return toEdges(await stmt.all());
 }
+// remove()/store() have already deleted rows by the time afterReconcile runs, so this records
+// whether any reconcile pass deleted at least one link row -- whether a file vanished, or a
+// reparse's stale rows shrank. dstChanged alone misses the reparsed-to-zero-links case (no
+// surviving rows to re-resolve). Keyed on the delta object, so the state dies with the reconcile.
+const removedWithLinks = new WeakMap();
 export const links = {
     name: 'links',
-    schema (db) {
-        db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');
-        db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');
-        db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');
+    async schema (db) {
+        await db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');
+        await db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');
+        await db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');
     },
     extract,
-    // Reparsed docs are diffed in store() below instead of wiped here: deleting and
-    // re-inserting resets dst to NULL, which made every touch-only reparse read as an edge
-    // change and recompute PageRank -- measured as most of the remaining update cost.
-    remove (db, path, delta) {
-        if (!vanishedSet(delta).has(path)) return;
-        const result = db.prepare('DELETE FROM links WHERE src = ?').run(path);
-        if (Number(result.changes) > 0) recordRemoved(delta, path);
+    // Reparsed docs are diffed in store() below instead of wiped here: deleting and re-inserting
+    // resets dst to NULL, which made every touch-only reparse read as an edge change and
+    // recompute PageRank -- measured as most of the remaining update cost. Only genuinely
+    // vanished files clear here.
+    async remove (db, paths, delta) {
+        const vanishedSet = new Set(delta.vanished);
+        const vanished = paths.filter((p)=>vanishedSet.has(p));
+        if (vanished.length === 0) return;
+        const existingRows = await selectIn(db, 'src', vanished);
+        await db.runBatch('DELETE FROM links WHERE src = ?', vanished.map((p)=>[
+                p
+            ]));
+        if (existingRows.length > 0) removedWithLinks.set(delta, true);
     },
-    store (db, path, extracted, delta) {
-        const targets = extracted;
-        // Stale rows (target/embed pairs the new parse no longer contains) are real edge removals.
-        // \0 can't appear in a target, so the composite key never collides.
-        let stale;
-        if (targets.length === 0) {
-            stale = db.prepare('DELETE FROM links WHERE src = ?').run(path);
-        } else {
-            const placeholders = targets.map(()=>'?').join(', ');
-            const keys = targets.map((t)=>`${t.target}\0${t.embed ? '1' : '0'}`);
-            stale = db.prepare(`DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (${placeholders})`).run(path, ...keys);
+    async store (db, docs, delta) {
+        const byPath = new Map(docs.map((d)=>[
+                d.path,
+                d.extracted
+            ]));
+        const addedSet = new Set(delta.added);
+        const reparsedExisting = docs.map((d)=>d.path).filter((p)=>!addedSet.has(p));
+        // Stale rows (existing target/embed pairs the new parse no longer contains) are real edge
+        // removals; diffed in JS from one bulk SELECT rather than a per-file NOT IN statement, so
+        // this whole pass costs one query plus one batched DELETE regardless of file count.
+        const existingRows = await selectIn(db, 'src', reparsedExisting);
+        const staleRows = existingRows.filter((row)=>{
+            var _byPath_get;
+            const targets = (_byPath_get = byPath.get(row.src)) !== null && _byPath_get !== void 0 ? _byPath_get : [];
+            return !targets.some((t)=>t.target === row.target && (t.embed ? 1 : 0) === row.embed);
+        });
+        if (staleRows.length > 0) {
+            await db.runBatch('DELETE FROM links WHERE src = ? AND target = ? AND embed = ?', staleRows.map((r)=>[
+                    r.src,
+                    r.target,
+                    r.embed
+                ]));
+            removedWithLinks.set(delta, true);
+        }
+        // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same value
+        // and reports no change; only genuinely new rows start at NULL. A same-note anchor's dst is
+        // always its own src, never another file's basename, so it gets no target_base -- SQL's
+        // `IN` never matches NULL, keeping it out of resolveIncremental's target_base lookup.
+        const upsertRows = [];
+        for (const [path, targets] of byPath){
+            for (const { target, embed } of targets)upsertRows.push([
+                path,
+                target,
+                target.startsWith('#') ? null : baseKey(cleanTarget(target)),
+                embed ? 1 : 0
+            ]);
+        }
+        if (upsertRows.length > 0) {
+            await db.runBatch('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base', upsertRows);
         }
-        if (Number(stale.changes) > 0) recordRemoved(delta, path);
-        // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same
-        // value and reports no change; only genuinely new rows start at NULL.
-        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');
-        // A same-note anchor's dst is always its own src, never another file's basename, so it
-        // gets no target_base -- SQL's `IN` never matches NULL, keeping it out of
-        // resolveIncremental's cross-file collectIn('target_base', ...) entirely.
-        for (const { target, embed } of targets)insert.run(path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0);
     },
-    afterReconcile (db, delta) {
-        var _ref;
+    async afterReconcile (db, delta) {
         var _removedWithLinks_get;
-        // Any deleted rows that carried edges mean the edge set shrank -- whether the file
-        // vanished or was reparsed down to fewer/no links. dstChanged alone misses the
-        // reparsed-to-zero-links case (no surviving rows to re-resolve).
-        const removeHadLinks = ((_ref = (_removedWithLinks_get = removedWithLinks.get(delta)) === null || _removedWithLinks_get === void 0 ? void 0 : _removedWithLinks_get.size) !== null && _ref !== void 0 ? _ref : 0) > 0;
+        // Any deleted rows mean the edge set shrank -- whether the file vanished or was reparsed
+        // down to fewer/no links.
+        const removeHadLinks = (_removedWithLinks_get = removedWithLinks.get(delta)) !== null && _removedWithLinks_get !== void 0 ? _removedWithLinks_get : false;
         const churn = delta.reparsed.length + delta.vanished.length;
         // Past this share of the tree, a full pass is the only one guaranteed to match
         // resolveTarget's ambiguity rules. A cold build clears the threshold on its own.
         const large = delta.files.length === 0 || churn > 0.2 * delta.files.length;
-        const dstChanged = large ? resolveAll(db, delta.files) : resolveIncremental(db, delta);
+        const dstChanged = large ? await resolveAll(db, delta.files) : await resolveIncremental(db, delta);
         delta.linksChanged = dstChanged || removeHadLinks;
     }
 };

package/dist/esm/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 type { FileStat } from '../scan/index.ts';\nimport { maskRegions } from './fences.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).\n// One rule for [[inner]] text wherever it appears: alias stripped after |, a leading #\n// keeps the anchor as the target (a same-note self-link needs a heading name), otherwise\n// the anchor splits off. 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 ? 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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 ? 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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// resolveTarget applied to `rows`, returning just the rows whose dst actually changed -- the\n// caller writes those in one runBatch call, keyed on (src, target) so a link/embed sibling\n// pair sharing one resolution rewrites both.\nfunction resolveRows(rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): LinkRow[] {\n  const changed: LinkRow[] = [];\n  for (const row of rows) {\n    const dst = resolveTarget(row.src, row.target, pathSet, byBase);\n    if (dst !== row.dst) changed.push({ ...row, dst });\n  }\n  return changed;\n}\n\nasync function writeResolved(db: Connection, rows: LinkRow[]): Promise<void> {\n  if (rows.length === 0) return;\n  await db.runBatch(\n    'UPDATE links SET dst = ? WHERE src = ? AND target = ?',\n    rows.map((r) => [r.dst, r.src, r.target])\n  );\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.\nasync function resolveAll(db: Connection, files: FileStat[]): Promise<boolean> {\n  const pathSet = new Set(files.map((f) => f.relPath));\n  const byBase = buildByBase(files);\n  const stmt = await db.prepare('SELECT src, target, dst, embed FROM links');\n  const rows = (await stmt.all()) as unknown as LinkRow[];\n  const changed = resolveRows(rows, pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\n// Chunked so a large-but-under-threshold delta never exceeds SQLite's bound-variable limit\n// (SQLITE_MAX_VARIABLE_NUMBER, 32766); harmless headroom on DuckDB, which has no such cap.\nasync function selectIn(db: Connection, column: string, keys: string[]): Promise<LinkRow[]> {\n  const rows: LinkRow[] = [];\n  for (let i = 0; i < keys.length; i += 500) {\n    const chunk = keys.slice(i, i + 500);\n    const stmt = await db.prepare(`SELECT src, target, dst, embed FROM links WHERE ${column} IN (${chunk.map(() => '?').join(', ')})`);\n    rows.push(...((await stmt.all(...chunk)) as unknown as LinkRow[]));\n  }\n  return rows;\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.\nasync function resolveIncremental(db: Connection, delta: ReconcileDelta): Promise<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  collect(await selectIn(db, 'src', delta.reparsed));\n  collect(await selectIn(db, 'target_base', [...changedBasenames]));\n  collect(await selectIn(db, 'dst', delta.vanished));\n\n  const changed = resolveRows([...candidates.values()], pathSet, byBase);\n  await writeResolved(db, changed);\n  return changed.length > 0;\n}\n\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. Exported (not just linkEdges below) so commands/signals.ts's async caller,\n// which only has the Store's prepare(), can run the identical statement itself.\nexport const LINK_EDGES_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\nexport function toEdges(rows: Array<{ src: string; dst: string }>): [string, string][] {\n  return rows.map((r) => [r.src, r.dst]);\n}\n\n// Resolved edges, for rank (inside reconcile's afterReconcile pass).\nexport async function linkEdges(db: Connection): Promise<[string, string][]> {\n  const stmt = await db.prepare(LINK_EDGES_SQL);\n  return toEdges((await stmt.all()) as Array<{ src: string; dst: string }>);\n}\n\n// remove()/store() have already deleted rows by the time afterReconcile runs, so this records\n// whether any reconcile pass deleted at least one link row -- whether a file vanished, or a\n// reparse's stale rows shrank. dstChanged alone misses the reparsed-to-zero-links case (no\n// surviving rows to re-resolve). Keyed on the delta object, so the state dies with the reconcile.\nconst removedWithLinks = new WeakMap<ReconcileDelta, boolean>();\n\nexport const links: Feature = {\n  name: 'links',\n  async schema(db) {\n    await 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    await db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    await 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 re-inserting\n  // resets dst to NULL, which made every touch-only reparse read as an edge change and\n  // recompute PageRank -- measured as most of the remaining update cost. Only genuinely\n  // vanished files clear here.\n  async remove(db, paths, delta) {\n    const vanishedSet = new Set(delta.vanished);\n    const vanished = paths.filter((p) => vanishedSet.has(p));\n    if (vanished.length === 0) return;\n    const existingRows = await selectIn(db, 'src', vanished);\n    await db.runBatch(\n      'DELETE FROM links WHERE src = ?',\n      vanished.map((p) => [p])\n    );\n    if (existingRows.length > 0) removedWithLinks.set(delta, true);\n  },\n  async store(db, docs: ExtractedDoc[], delta) {\n    const byPath = new Map(docs.map((d) => [d.path, d.extracted as Array<{ target: string; embed: boolean }>]));\n    const addedSet = new Set(delta.added);\n    const reparsedExisting = docs.map((d) => d.path).filter((p) => !addedSet.has(p));\n\n    // Stale rows (existing target/embed pairs the new parse no longer contains) are real edge\n    // removals; diffed in JS from one bulk SELECT rather than a per-file NOT IN statement, so\n    // this whole pass costs one query plus one batched DELETE regardless of file count.\n    const existingRows = await selectIn(db, 'src', reparsedExisting);\n    const staleRows = existingRows.filter((row) => {\n      const targets = byPath.get(row.src) ?? [];\n      return !targets.some((t) => t.target === row.target && (t.embed ? 1 : 0) === row.embed);\n    });\n    if (staleRows.length > 0) {\n      await db.runBatch(\n        'DELETE FROM links WHERE src = ? AND target = ? AND embed = ?',\n        staleRows.map((r) => [r.src, r.target, r.embed])\n      );\n      removedWithLinks.set(delta, true);\n    }\n\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same value\n    // and reports no change; only genuinely new rows start at NULL. A same-note anchor's dst is\n    // always its own src, never another file's basename, so it gets no target_base -- SQL's\n    // `IN` never matches NULL, keeping it out of resolveIncremental's target_base lookup.\n    const upsertRows: unknown[][] = [];\n    for (const [path, targets] of byPath) {\n      for (const { target, embed } of targets) upsertRows.push([path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0]);\n    }\n    if (upsertRows.length > 0) {\n      await db.runBatch('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base', upsertRows);\n    }\n  },\n  async afterReconcile(db, delta) {\n    // Any deleted rows mean the edge set shrank -- whether the file vanished or was reparsed\n    // down to fewer/no links.\n    const removeHadLinks = removedWithLinks.get(delta) ?? false;\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 ? await resolveAll(db, delta.files) : await resolveIncremental(db, delta);\n    delta.linksChanged = dstChanged || removeHadLinks;\n  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package/dist/esm/features/rank.js

@@ -4,17 +4,24 @@ import { linkEdges } from './links.js';
 // note" prior. Depends on links (enforced in config.featureEnabled).
 export const rank = {
     name: 'rank',
-    schema (db) {
-        const columns = db.prepare('PRAGMA table_info(frontmatter)').all();
-        if (!columns.some((c)=>c.name === '_rank')) db.exec('ALTER TABLE frontmatter ADD COLUMN "_rank" REAL');
+    async schema (db) {
+        const stmt = await db.prepare('PRAGMA table_info(frontmatter)');
+        const columns = await stmt.all();
+        if (!columns.some((c)=>c.name === '_rank')) await db.exec('ALTER TABLE frontmatter ADD COLUMN "_rank" REAL');
     },
-    afterReconcile (db, delta) {
+    async afterReconcile (db, delta) {
         // Only an explicit linksChanged:false skips. Rank also depends on the node set, so any
         // add or vanish recomputes -- otherwise a new linkless note keeps _rank NULL.
         if (delta.linksChanged === false && delta.added.length === 0 && delta.vanished.length === 0) return;
-        const nodes = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
-        const ranks = pagerank(nodes, linkEdges(db));
-        const update = db.prepare('UPDATE frontmatter SET "_rank" = ? WHERE "path" = ?');
-        for (const [path, value] of ranks)update.run(value, path);
+        const pathsStmt = await db.prepare('SELECT "path" FROM frontmatter');
+        const nodes = (await pathsStmt.all()).map((r)=>r.path);
+        const ranks = pagerank(nodes, await linkEdges(db));
+        if (ranks.size === 0) return;
+        await db.runBatch('UPDATE frontmatter SET "_rank" = ? WHERE "path" = ?', [
+            ...ranks
+        ].map(([path, value])=>[
+                value,
+                path
+            ]));
     }
 };

package/dist/esm/features/rank.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/rank.ts"],"sourcesContent":["import { pagerank } from '../graph/graph.ts';\nimport { linkEdges } from './links.ts';\nimport type { Feature } from './types.ts';\n\n// frontmatter._rank: PageRank over resolved links -- a static \"how load-bearing is this\n// note\" prior. Depends on links (enforced in config.featureEnabled).\n\nexport const rank: Feature = {\n  name: 'rank',\n  schema(db) {\n    const columns = db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>;\n    if (!columns.some((c) => c.name === '_rank')) db.exec('ALTER TABLE frontmatter ADD COLUMN \"_rank\" REAL');\n  },\n  afterReconcile(db, delta) {\n    // Only an explicit linksChanged:false skips. Rank also depends on the node set, so any\n    // add or vanish recomputes -- otherwise a new linkless note keeps _rank NULL.\n    if (delta.linksChanged === false && delta.added.length === 0 && delta.vanished.length === 0) return;\n    const nodes = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n    const ranks = pagerank(nodes, linkEdges(db));\n    const update = db.prepare('UPDATE frontmatter SET \"_rank\" = ? WHERE \"path\" = ?');\n    for (const [path, value] of ranks) update.run(value, path);\n  },\n};\n"],"names":["pagerank","linkEdges","rank","name","schema","db","columns","prepare","all","some","c","exec","afterReconcile","delta","linksChanged","added","length","vanished","nodes","map","r","path","ranks","update","value","run"],"mappings":"AAAA,SAASA,QAAQ,QAAQ,oBAAoB;AAC7C,SAASC,SAAS,QAAQ,aAAa;AAGvC,wFAAwF;AACxF,qEAAqE;AAErE,OAAO,MAAMC,OAAgB;IAC3BC,MAAM;IACNC,QAAOC,EAAE;QACP,MAAMC,UAAUD,GAAGE,OAAO,CAAC,kCAAkCC,GAAG;QAChE,IAAI,CAACF,QAAQG,IAAI,CAAC,CAACC,IAAMA,EAAEP,IAAI,KAAK,UAAUE,GAAGM,IAAI,CAAC;IACxD;IACAC,gBAAeP,EAAE,EAAEQ,KAAK;QACtB,uFAAuF;QACvF,8EAA8E;QAC9E,IAAIA,MAAMC,YAAY,KAAK,SAASD,MAAME,KAAK,CAACC,MAAM,KAAK,KAAKH,MAAMI,QAAQ,CAACD,MAAM,KAAK,GAAG;QAC7F,MAAME,QAAQ,AAACb,GAAGE,OAAO,CAAC,kCAAkCC,GAAG,GAA+BW,GAAG,CAAC,CAACC,IAAMA,EAAEC,IAAI;QAC/G,MAAMC,QAAQtB,SAASkB,OAAOjB,UAAUI;QACxC,MAAMkB,SAASlB,GAAGE,OAAO,CAAC;QAC1B,KAAK,MAAM,CAACc,MAAMG,MAAM,IAAIF,MAAOC,OAAOE,GAAG,CAACD,OAAOH;IACvD;AACF,EAAE"}
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/rank.ts"],"sourcesContent":["import { pagerank } from '../graph/graph.ts';\nimport { linkEdges } from './links.ts';\nimport type { Feature } from './types.ts';\n\n// frontmatter._rank: PageRank over resolved links -- a static \"how load-bearing is this\n// note\" prior. Depends on links (enforced in config.featureEnabled).\n\nexport const rank: Feature = {\n  name: 'rank',\n  async schema(db) {\n    const stmt = await db.prepare('PRAGMA table_info(frontmatter)');\n    const columns = (await stmt.all()) as Array<{ name: string }>;\n    if (!columns.some((c) => c.name === '_rank')) await db.exec('ALTER TABLE frontmatter ADD COLUMN \"_rank\" REAL');\n  },\n  async afterReconcile(db, delta) {\n    // Only an explicit linksChanged:false skips. Rank also depends on the node set, so any\n    // add or vanish recomputes -- otherwise a new linkless note keeps _rank NULL.\n    if (delta.linksChanged === false && delta.added.length === 0 && delta.vanished.length === 0) return;\n    const pathsStmt = await db.prepare('SELECT \"path\" FROM frontmatter');\n    const nodes = ((await pathsStmt.all()) as Array<{ path: string }>).map((r) => r.path);\n    const ranks = pagerank(nodes, await linkEdges(db));\n    if (ranks.size === 0) return;\n    await db.runBatch(\n      'UPDATE frontmatter SET \"_rank\" = ? WHERE \"path\" = ?',\n      [...ranks].map(([path, value]) => [value, path])\n    );\n  },\n};\n"],"names":["pagerank","linkEdges","rank","name","schema","db","stmt","prepare","columns","all","some","c","exec","afterReconcile","delta","linksChanged","added","length","vanished","pathsStmt","nodes","map","r","path","ranks","size","runBatch","value"],"mappings":"AAAA,SAASA,QAAQ,QAAQ,oBAAoB;AAC7C,SAASC,SAAS,QAAQ,aAAa;AAGvC,wFAAwF;AACxF,qEAAqE;AAErE,OAAO,MAAMC,OAAgB;IAC3BC,MAAM;IACN,MAAMC,QAAOC,EAAE;QACb,MAAMC,OAAO,MAAMD,GAAGE,OAAO,CAAC;QAC9B,MAAMC,UAAW,MAAMF,KAAKG,GAAG;QAC/B,IAAI,CAACD,QAAQE,IAAI,CAAC,CAACC,IAAMA,EAAER,IAAI,KAAK,UAAU,MAAME,GAAGO,IAAI,CAAC;IAC9D;IACA,MAAMC,gBAAeR,EAAE,EAAES,KAAK;QAC5B,uFAAuF;QACvF,8EAA8E;QAC9E,IAAIA,MAAMC,YAAY,KAAK,SAASD,MAAME,KAAK,CAACC,MAAM,KAAK,KAAKH,MAAMI,QAAQ,CAACD,MAAM,KAAK,GAAG;QAC7F,MAAME,YAAY,MAAMd,GAAGE,OAAO,CAAC;QACnC,MAAMa,QAAQ,AAAE,CAAA,MAAMD,UAAUV,GAAG,EAAC,EAA+BY,GAAG,CAAC,CAACC,IAAMA,EAAEC,IAAI;QACpF,MAAMC,QAAQxB,SAASoB,OAAO,MAAMnB,UAAUI;QAC9C,IAAImB,MAAMC,IAAI,KAAK,GAAG;QACtB,MAAMpB,GAAGqB,QAAQ,CACf,uDACA;eAAIF;SAAM,CAACH,GAAG,CAAC,CAAC,CAACE,MAAMI,MAAM,GAAK;gBAACA;gBAAOJ;aAAK;IAEnD;AACF,EAAE"}

package/dist/esm/features/sections.js

@@ -26,15 +26,28 @@ function extract(raw) {
 }
 export const sections = {
     name: 'sections',
-    schema (db) {
-        db.exec(`CREATE TABLE IF NOT EXISTS sections ("path" TEXT, idx INTEGER, level INTEGER, heading TEXT, start_line INTEGER, end_line INTEGER, tokens INTEGER, PRIMARY KEY ("path", idx))`);
+    async schema (db) {
+        await db.exec(`CREATE TABLE IF NOT EXISTS sections ("path" TEXT, idx INTEGER, level INTEGER, heading TEXT, start_line INTEGER, end_line INTEGER, tokens INTEGER, PRIMARY KEY ("path", idx))`);
     },
     extract,
-    remove (db, path) {
-        db.prepare('DELETE FROM sections WHERE "path" = ?').run(path);
+    async remove (db, paths) {
+        if (paths.length === 0) return;
+        await db.runBatch('DELETE FROM sections WHERE "path" = ?', paths.map((p)=>[
+                p
+            ]));
     },
-    store (db, path, extracted) {
-        const insert = db.prepare('INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?)');
-        extracted.forEach((s, idx)=>insert.run(path, idx, s.level, s.heading, s.startLine, s.endLine, s.tokens));
+    async store (db, docs) {
+        const rows = [];
+        for (const { path, extracted } of docs)extracted.forEach((s, idx)=>rows.push([
+                path,
+                idx,
+                s.level,
+                s.heading,
+                s.startLine,
+                s.endLine,
+                s.tokens
+            ]));
+        if (rows.length === 0) return;
+        await db.runBatch('INSERT INTO sections ("path", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?)', rows);
     }
 };

package/dist/esm/features/sections.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/sections.ts"],"sourcesContent":["import { estimateTokens } from '../chunk/index.ts';\nimport { fenceTracker } from './fences.ts';\nimport type { Feature } from './types.ts';\n\n// sections(path, idx, level, heading, start_line, end_line, tokens): the heading outline,\n// 1-indexed over the raw file so a row is a direct Read range; tokens is estimateTokens (D5),\n// CJK-aware rather than a flat chars/4.\n\nexport interface Section {\n  level: number;\n  heading: string;\n  startLine: number;\n  endLine: number;\n  tokens: number;\n}\n\n// Headings outside fenced code blocks.\nfunction extract(raw: string): Section[] {\n  const lines = raw.split('\\n');\n  const found: Section[] = [];\n  const fence = fenceTracker();\n  for (let i = 0; i < lines.length; i++) {\n    if (fence.feed(lines[i])) continue;\n    if (fence.inFence) continue;\n    const m = lines[i].match(/^(#{1,6}) +(.*)/);\n    if (m) found.push({ level: m[1].length, heading: m[2].trim(), startLine: i + 1, endLine: lines.length, tokens: 0 });\n  }\n  for (let s = 0; s < found.length; s++) {\n    if (s + 1 < found.length) found[s].endLine = found[s + 1].startLine - 1;\n    const text = lines.slice(found[s].startLine - 1, found[s].endLine).join('\\n');\n    found[s].tokens = Math.ceil(estimateTokens(text));\n  }\n  return found;\n}\n\nexport const sections: Feature = {\n  name: 'sections',\n  schema(db) {\n    db.exec(`CREATE TABLE IF NOT EXISTS sections (\"path\" TEXT, idx INTEGER, level INTEGER, heading TEXT, start_line INTEGER, end_line INTEGER, tokens INTEGER, PRIMARY KEY (\"path\", idx))`);\n  },\n  extract,\n  remove(db, path) {\n    db.prepare('DELETE FROM sections WHERE \"path\" = ?').run(path);\n  },\n  store(db, path, extracted) {\n    const insert = db.prepare('INSERT INTO sections (\"path\", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?)');\n    (extracted as Section[]).forEach((s, idx) => insert.run(path, idx, s.level, s.heading, s.startLine, s.endLine, s.tokens));\n  },\n};\n"],"names":["estimateTokens","fenceTracker","extract","raw","lines","split","found","fence","i","length","feed","inFence","m","match","push","level","heading","trim","startLine","endLine","tokens","s","text","slice","join","Math","ceil","sections","name","schema","db","exec","remove","path","prepare","run","store","extracted","insert","forEach","idx"],"mappings":"AAAA,SAASA,cAAc,QAAQ,oBAAoB;AACnD,SAASC,YAAY,QAAQ,cAAc;AAe3C,uCAAuC;AACvC,SAASC,QAAQC,GAAW;IAC1B,MAAMC,QAAQD,IAAIE,KAAK,CAAC;IACxB,MAAMC,QAAmB,EAAE;IAC3B,MAAMC,QAAQN;IACd,IAAK,IAAIO,IAAI,GAAGA,IAAIJ,MAAMK,MAAM,EAAED,IAAK;QACrC,IAAID,MAAMG,IAAI,CAACN,KAAK,CAACI,EAAE,GAAG;QAC1B,IAAID,MAAMI,OAAO,EAAE;QACnB,MAAMC,IAAIR,KAAK,CAACI,EAAE,CAACK,KAAK,CAAC;QACzB,IAAID,GAAGN,MAAMQ,IAAI,CAAC;YAAEC,OAAOH,CAAC,CAAC,EAAE,CAACH,MAAM;YAAEO,SAASJ,CAAC,CAAC,EAAE,CAACK,IAAI;YAAIC,WAAWV,IAAI;YAAGW,SAASf,MAAMK,MAAM;YAAEW,QAAQ;QAAE;IACnH;IACA,IAAK,IAAIC,IAAI,GAAGA,IAAIf,MAAMG,MAAM,EAAEY,IAAK;QACrC,IAAIA,IAAI,IAAIf,MAAMG,MAAM,EAAEH,KAAK,CAACe,EAAE,CAACF,OAAO,GAAGb,KAAK,CAACe,IAAI,EAAE,CAACH,SAAS,GAAG;QACtE,MAAMI,OAAOlB,MAAMmB,KAAK,CAACjB,KAAK,CAACe,EAAE,CAACH,SAAS,GAAG,GAAGZ,KAAK,CAACe,EAAE,CAACF,OAAO,EAAEK,IAAI,CAAC;QACxElB,KAAK,CAACe,EAAE,CAACD,MAAM,GAAGK,KAAKC,IAAI,CAAC1B,eAAesB;IAC7C;IACA,OAAOhB;AACT;AAEA,OAAO,MAAMqB,WAAoB;IAC/BC,MAAM;IACNC,QAAOC,EAAE;QACPA,GAAGC,IAAI,CAAC,CAAC,4KAA4K,CAAC;IACxL;IACA7B;IACA8B,QAAOF,EAAE,EAAEG,IAAI;QACbH,GAAGI,OAAO,CAAC,yCAAyCC,GAAG,CAACF;IAC1D;IACAG,OAAMN,EAAE,EAAEG,IAAI,EAAEI,SAAS;QACvB,MAAMC,SAASR,GAAGI,OAAO,CAAC;QACzBG,UAAwBE,OAAO,CAAC,CAAClB,GAAGmB,MAAQF,OAAOH,GAAG,CAACF,MAAMO,KAAKnB,EAAEN,KAAK,EAAEM,EAAEL,OAAO,EAAEK,EAAEH,SAAS,EAAEG,EAAEF,OAAO,EAAEE,EAAED,MAAM;IACzH;AACF,EAAE"}
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/sections.ts"],"sourcesContent":["import { estimateTokens } from '../chunk/index.ts';\nimport { fenceTracker } from './fences.ts';\nimport type { Feature } from './types.ts';\n\n// sections(path, idx, level, heading, start_line, end_line, tokens): the heading outline,\n// 1-indexed over the raw file so a row is a direct Read range; tokens is estimateTokens (D5),\n// CJK-aware rather than a flat chars/4.\n\nexport interface Section {\n  level: number;\n  heading: string;\n  startLine: number;\n  endLine: number;\n  tokens: number;\n}\n\n// Headings outside fenced code blocks.\nfunction extract(raw: string): Section[] {\n  const lines = raw.split('\\n');\n  const found: Section[] = [];\n  const fence = fenceTracker();\n  for (let i = 0; i < lines.length; i++) {\n    if (fence.feed(lines[i])) continue;\n    if (fence.inFence) continue;\n    const m = lines[i].match(/^(#{1,6}) +(.*)/);\n    if (m) found.push({ level: m[1].length, heading: m[2].trim(), startLine: i + 1, endLine: lines.length, tokens: 0 });\n  }\n  for (let s = 0; s < found.length; s++) {\n    if (s + 1 < found.length) found[s].endLine = found[s + 1].startLine - 1;\n    const text = lines.slice(found[s].startLine - 1, found[s].endLine).join('\\n');\n    found[s].tokens = Math.ceil(estimateTokens(text));\n  }\n  return found;\n}\n\nexport const sections: Feature = {\n  name: 'sections',\n  async schema(db) {\n    await db.exec(`CREATE TABLE IF NOT EXISTS sections (\"path\" TEXT, idx INTEGER, level INTEGER, heading TEXT, start_line INTEGER, end_line INTEGER, tokens INTEGER, PRIMARY KEY (\"path\", idx))`);\n  },\n  extract,\n  async remove(db, paths) {\n    if (paths.length === 0) return;\n    await db.runBatch(\n      'DELETE FROM sections WHERE \"path\" = ?',\n      paths.map((p) => [p])\n    );\n  },\n  async store(db, docs) {\n    const rows: unknown[][] = [];\n    for (const { path, extracted } of docs) (extracted as Section[]).forEach((s, idx) => rows.push([path, idx, s.level, s.heading, s.startLine, s.endLine, s.tokens]));\n    if (rows.length === 0) return;\n    await db.runBatch('INSERT INTO sections (\"path\", idx, level, heading, start_line, end_line, tokens) VALUES (?, ?, ?, ?, ?, ?, ?)', rows);\n  },\n};\n"],"names":["estimateTokens","fenceTracker","extract","raw","lines","split","found","fence","i","length","feed","inFence","m","match","push","level","heading","trim","startLine","endLine","tokens","s","text","slice","join","Math","ceil","sections","name","schema","db","exec","remove","paths","runBatch","map","p","store","docs","rows","path","extracted","forEach","idx"],"mappings":"AAAA,SAASA,cAAc,QAAQ,oBAAoB;AACnD,SAASC,YAAY,QAAQ,cAAc;AAe3C,uCAAuC;AACvC,SAASC,QAAQC,GAAW;IAC1B,MAAMC,QAAQD,IAAIE,KAAK,CAAC;IACxB,MAAMC,QAAmB,EAAE;IAC3B,MAAMC,QAAQN;IACd,IAAK,IAAIO,IAAI,GAAGA,IAAIJ,MAAMK,MAAM,EAAED,IAAK;QACrC,IAAID,MAAMG,IAAI,CAACN,KAAK,CAACI,EAAE,GAAG;QAC1B,IAAID,MAAMI,OAAO,EAAE;QACnB,MAAMC,IAAIR,KAAK,CAACI,EAAE,CAACK,KAAK,CAAC;QACzB,IAAID,GAAGN,MAAMQ,IAAI,CAAC;YAAEC,OAAOH,CAAC,CAAC,EAAE,CAACH,MAAM;YAAEO,SAASJ,CAAC,CAAC,EAAE,CAACK,IAAI;YAAIC,WAAWV,IAAI;YAAGW,SAASf,MAAMK,MAAM;YAAEW,QAAQ;QAAE;IACnH;IACA,IAAK,IAAIC,IAAI,GAAGA,IAAIf,MAAMG,MAAM,EAAEY,IAAK;QACrC,IAAIA,IAAI,IAAIf,MAAMG,MAAM,EAAEH,KAAK,CAACe,EAAE,CAACF,OAAO,GAAGb,KAAK,CAACe,IAAI,EAAE,CAACH,SAAS,GAAG;QACtE,MAAMI,OAAOlB,MAAMmB,KAAK,CAACjB,KAAK,CAACe,EAAE,CAACH,SAAS,GAAG,GAAGZ,KAAK,CAACe,EAAE,CAACF,OAAO,EAAEK,IAAI,CAAC;QACxElB,KAAK,CAACe,EAAE,CAACD,MAAM,GAAGK,KAAKC,IAAI,CAAC1B,eAAesB;IAC7C;IACA,OAAOhB;AACT;AAEA,OAAO,MAAMqB,WAAoB;IAC/BC,MAAM;IACN,MAAMC,QAAOC,EAAE;QACb,MAAMA,GAAGC,IAAI,CAAC,CAAC,4KAA4K,CAAC;IAC9L;IACA7B;IACA,MAAM8B,QAAOF,EAAE,EAAEG,KAAK;QACpB,IAAIA,MAAMxB,MAAM,KAAK,GAAG;QACxB,MAAMqB,GAAGI,QAAQ,CACf,yCACAD,MAAME,GAAG,CAAC,CAACC,IAAM;gBAACA;aAAE;IAExB;IACA,MAAMC,OAAMP,EAAE,EAAEQ,IAAI;QAClB,MAAMC,OAAoB,EAAE;QAC5B,KAAK,MAAM,EAAEC,IAAI,EAAEC,SAAS,EAAE,IAAIH,KAAM,AAACG,UAAwBC,OAAO,CAAC,CAACrB,GAAGsB,MAAQJ,KAAKzB,IAAI,CAAC;gBAAC0B;gBAAMG;gBAAKtB,EAAEN,KAAK;gBAAEM,EAAEL,OAAO;gBAAEK,EAAEH,SAAS;gBAAEG,EAAEF,OAAO;gBAAEE,EAAED,MAAM;aAAC;QAChK,IAAImB,KAAK9B,MAAM,KAAK,GAAG;QACvB,MAAMqB,GAAGI,QAAQ,CAAC,iHAAiHK;IACrI;AACF,EAAE"}