sensemaking 0.15.0 → 0.15.2

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

@@ -1 +1 @@
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Skipped when there\n    // is no comment marker anywhere near this line -- most lines, so worth the branch.\n    const masked = comment.inComment || line.includes('<!--') ? comment.mask(line) : line;\n    // Indented or blockquoted HTML blocks still swallow their content in Obsidian, so the\n    // opener test runs after stripping leading whitespace and > markers.\n    const stripped = masked.replace(/^[ \\t>]*/, '');\n    if (stripped[0] === '<') {\n      const openMatch = HTML_BLOCK_OPEN_RE.exec(stripped);\n      if (openMatch) {\n        const tagName = openMatch[1].toLowerCase();\n        const isClosingTag = stripped[1] === '/';\n        if (!isClosingTag && HTML_PRE_TAGS.has(tagName)) {\n          inHtmlBlock = true;\n          // Any of the four type-1 closers ends the block, not only the tag that opened it.\n          htmlBlockClose = /<\\/(?:script|pre|style|textarea)>/i;\n          continue;\n        }\n        if (HTML_BLOCK_TAGS.has(tagName)) {\n          inHtmlBlock = true;\n          continue;\n        }\n      }\n    }\n    if (!masked.includes('#')) continue; // most lines; skip the regex work\n    let cleaned = masked.includes('`') ? maskCodeSpans(masked) : masked;\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

@@ -3,3 +3,10 @@ export interface FenceTracker {
     readonly inFence: boolean;
 }
 export declare function fenceTracker(): FenceTracker;
+export interface CommentTracker {
+    mask(line: string): string;
+    readonly inComment: boolean;
+}
+export declare function commentTracker(): CommentTracker;
+export declare function maskRegions(body: string): string;
+export declare function maskCodeSpans(line: string): string;

package/dist/cjs/fences.d.ts

@@ -3,3 +3,10 @@ export interface FenceTracker {
     readonly inFence: boolean;
 }
 export declare function fenceTracker(): FenceTracker;
+export interface CommentTracker {
+    mask(line: string): string;
+    readonly inComment: boolean;
+}
+export declare function commentTracker(): CommentTracker;
+export declare function maskRegions(body: string): string;
+export declare function maskCodeSpans(line: string): string;

package/dist/cjs/fences.js

@@ -7,10 +7,24 @@
 Object.defineProperty(exports, "__esModule", {
     value: true
 });
-Object.defineProperty(exports, "fenceTracker", {
-    enumerable: true,
-    get: function() {
+function _export(target, all) {
+    for(var name in all)Object.defineProperty(target, name, {
+        enumerable: true,
+        get: Object.getOwnPropertyDescriptor(all, name).get
+    });
+}
+_export(exports, {
+    get commentTracker () {
+        return commentTracker;
+    },
+    get fenceTracker () {
         return fenceTracker;
+    },
+    get maskCodeSpans () {
+        return maskCodeSpans;
+    },
+    get maskRegions () {
+        return maskRegions;
     }
 });
 var BACKTICK_OPEN = /^(`{3,})(.*)$/;
@@ -51,4 +65,93 @@ function fenceTracker() {
         }
     };
 }
+function commentTracker() {
+    var inComment = false;
+    return {
+        mask: function mask(line) {
+            var out = '';
+            var i = 0;
+            while(i < line.length){
+                if (inComment) {
+                    var end = line.indexOf('-->', i);
+                    if (end === -1) {
+                        out += ' '.repeat(line.length - i);
+                        i = line.length;
+                    } else {
+                        out += ' '.repeat(end + 3 - i);
+                        i = end + 3;
+                        inComment = false;
+                    }
+                    continue;
+                }
+                var start = line.indexOf('<!--', i);
+                if (start === -1) {
+                    out += line.slice(i);
+                    i = line.length;
+                } else {
+                    out += "".concat(line.slice(i, start), "    ");
+                    i = start + 4;
+                    inComment = true;
+                }
+            }
+            return out;
+        },
+        get inComment () {
+            return inComment;
+        }
+    };
+}
+function maskRegions(body) {
+    if (!/[`~]/.test(body) && !body.includes('<!--')) return body;
+    var fence = fenceTracker();
+    var comment = commentTracker();
+    return body.split('\n').map(function(line) {
+        if (!comment.inComment) {
+            var isDelim = fence.feed(line);
+            if (isDelim || fence.inFence) return ' '.repeat(line.length);
+        }
+        var uncommented = comment.mask(line);
+        // Inline code spans hide their content too: `[[x]]` in prose is not a link.
+        return uncommented.includes('`') ? maskCodeSpans(uncommented) : uncommented;
+    }).join('\n');
+}
+function maskCodeSpans(line) {
+    var out = '';
+    var i = 0;
+    while(i < line.length){
+        if (line[i] !== '`') {
+            out += line[i];
+            i++;
+            continue;
+        }
+        var j = i;
+        while(line[j] === '`')j++;
+        var n = j - i;
+        var k = j;
+        var closeStart = -1;
+        var closeEnd = -1;
+        while(k < line.length){
+            if (line[k] !== '`') {
+                k++;
+                continue;
+            }
+            var m = k;
+            while(line[m] === '`')m++;
+            if (m - k === n) {
+                closeStart = k;
+                closeEnd = m;
+                break;
+            }
+            k = m;
+        }
+        if (closeStart >= 0) {
+            out += ' '.repeat(closeEnd - i);
+            i = closeEnd;
+        } else {
+            out += line.slice(i, j);
+            i = j;
+        }
+    }
+    return out;
+}
 /* CJS INTEROP */ if (exports.__esModule && exports.default) { try { Object.defineProperty(exports.default, '__esModule', { value: true }); for (var key in exports) { exports.default[key] = exports[key]; } } catch (_) {}; module.exports = exports.default; }

package/dist/cjs/fences.js.map

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package/dist/esm/commands/peek.js

@@ -34,13 +34,13 @@ export function peek(db, cfg, pathArg, overrides = {}) {
     let backlinksTotal = 0;
     const _allowed = scopedPaths(db, cfg, overrides);
     if (featureEnabled(cfg, 'links')) {
-        const out = db.prepare('SELECT target, dst FROM links WHERE src = ? ORDER BY target').all(path);
+        const out = db.prepare('SELECT target, dst FROM links WHERE src = ? AND (dst IS NULL OR dst != src) ORDER BY target').all(path);
         outbound = [
             ...new Set(out.filter((l)=>l.dst !== null).map((l)=>l.dst))
         ];
         unresolved = out.filter((l)=>l.dst === null).map((l)=>l.target);
-        backlinksTotal = db.prepare('SELECT COUNT(DISTINCT src) AS n FROM links WHERE dst = ?').get(path).n;
-        backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? ORDER BY src LIMIT ?').all(path, PEEK_LIST_LIMIT).map((r)=>r.src);
+        backlinksTotal = db.prepare('SELECT COUNT(DISTINCT src) AS n FROM links WHERE dst = ? AND src != dst').get(path).n;
+        backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? AND src != dst ORDER BY src LIMIT ?').all(path, PEEK_LIST_LIMIT).map((r)=>r.src);
     }
     return {
         path,

package/dist/esm/commands/peek.js.map

@@ -1 +1 @@
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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/commands/peek.ts"],"sourcesContent":["import posix from 'node:path/posix';\nimport type { DatabaseSync } from 'node:sqlite';\nimport type { FeatureName, ResolvedConfig, SearchOverrides } from '../config/index.ts';\nimport { featureEnabled } from '../config/index.ts';\nimport { SenseError } from '../errors.ts';\nimport type { Row } from '../output.ts';\nimport { INTERNAL_COLUMNS, scopedPaths } from './scope.ts';\n\n// Note resolution shared by peek and path: an exact path, or a unique basename (case\n// insensitive, .md stripped).\nexport function resolveNote(paths: string[], arg: string): string {\n  const exact = paths.find((p) => p === arg);\n  if (exact) return exact;\n  const base = posix.basename(arg).replace(/\\.md$/i, '').toLowerCase();\n  const matches = paths.filter((p) => posix.basename(p).replace(/\\.md$/i, '').toLowerCase() === base);\n  if (matches.length === 1) return matches[0];\n  if (matches.length > 1) throw new SenseError('NOTE_AMBIGUOUS', `\"${arg}\" is ambiguous: ${matches.join(', ')}`);\n  throw new SenseError('NOTE_NOT_FOUND', `no note matches \"${arg}\"`);\n}\n\nexport interface Peek {\n  path: string;\n  tokens: number;\n  frontmatter: Row;\n  // Set when the note's frontmatter was refused, so an empty frontmatter block reads as \"did\n  // not parse\" rather than \"has none\". 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Query the sections/links tables\n  // directly for the full list.\n  sectionsTotal: number;\n  outboundTotal: number;\n  backlinksTotal: number;\n  unresolvedTotal: number;\n  // Bounded k-hop expansion beyond the immediate ring already shown by outbound/backlinks\n  // (depth starts at 2).\n  off: FeatureName[]; // disabled features whose blocks are omitted (not empty)\n}\n\nconst PEEK_LIST_LIMIT = 20;\n\n// peek: everything about one note except its prose -- frontmatter, outline with line\n// ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.\nexport function peek(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string, overrides: SearchOverrides = {}): Peek {\n  const paths = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  const path = resolveNote(paths, pathArg);\n\n  const row = db.prepare('SELECT * FROM frontmatter WHERE \"path\" = ?').get(path) as Row;\n  const parseError = (row._parse_error as string | null) ?? null;\n  const frontmatter: Row = {};\n  for (const [key, value] of Object.entries(row)) {\n    if (!INTERNAL_COLUMNS.has(key) && value !== null) frontmatter[key] = value;\n  }\n\n  const sectionsTotal = featureEnabled(cfg, 'sections') ? 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package/dist/esm/commands/related.js

@@ -8,8 +8,8 @@ import { scopedPaths, scopeHasEmbeddings } from './scope.js';
 export async function relatedNotes(db, cfg, pathArg, overrides, k) {
     const paths = db.prepare('SELECT "path" FROM frontmatter').all().map((r)=>r.path);
     const path = resolveNote(paths, pathArg);
-    const outbound = db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL').all(path).map((r)=>r.dst);
-    const backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ?').all(path).map((r)=>r.src);
+    const outbound = db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL AND dst != src').all(path).map((r)=>r.dst);
+    const backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? AND src != dst').all(path).map((r)=>r.src);
     const exclude = new Set([
         path,
         ...outbound,

package/dist/esm/commands/related.js.map

@@ -1 +1 @@
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package/dist/esm/db/open.d.ts

@@ -1,7 +1,7 @@
 import { DatabaseSync } from 'node:sqlite';
 import type { ResolvedConfig } from '../config/index.js';
 export declare const DB_FILENAME = "cache.db";
-export declare const SCHEMA_VERSION = "15";
+export declare const SCHEMA_VERSION = "16";
 export interface OpenResult {
     db: DatabaseSync;
     cfg: ResolvedConfig;

package/dist/esm/db/open.js

@@ -12,7 +12,7 @@ import { getMeta, setMeta } from './shared.js';
 export const DB_FILENAME = 'cache.db';
 // Cache shape version, independent of the config's own `version`. Bumping it rebuilds
 // existing trees on first query.
-export const SCHEMA_VERSION = '15';
+export const SCHEMA_VERSION = '16';
 // Stemming is English-only, but the segmentation underneath it is what decides coverage:
 // unicode61 splits on spaces, so a language written without them (Chinese, Japanese, Thai)
 // indexes a whole run as one token and word search finds nothing. `content.tokenize` is how

package/dist/esm/db/open.js.map

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/db/open.ts"],"sourcesContent":["// The Node floor (>=22.20) is explained here and nowhere else: 22.20 is the first release with\n// both FTS5 and row-returning INSERT ... RETURNING. Raise it only for a load-bearing capability.\nimport { mkdirSync, rmSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { DatabaseSync } from 'node:sqlite';\nimport type { Config, ResolvedConfig } from '../config/index.ts';\nimport { contentTokenize, featureSignature, STATE_DIR } from '../config/index.ts';\nimport { SenseError } from '../errors.ts';\nimport { activeFeatures } from '../features/index.ts';\nimport { registerFunctions } from '../sql-functions.ts';\nimport { changedSignatureKeys, rebuildContentTable, reconcile, signatureDiff } from './reconcile.ts';\nimport { getMeta, setMeta } from './shared.ts';\n\nexport const DB_FILENAME = 'cache.db';\n// Cache shape version, independent of the config's own `version`. 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NULL when the table does not exist yet.\nfunction storedTokenize(db: DatabaseSync): string | null {\n  const row = db.prepare(`SELECT sql FROM sqlite_master WHERE name = 'content'`).get() as { sql: string } | undefined;\n  if (!row) return null;\n  const m = row.sql.match(/tokenize = '((?:[^']|'')*)'/);\n  return m ? m[1] : null;\n}\n\n// Content is a separate table (not a column on frontmatter) so `SELECT * FROM frontmatter`\n// can't dump file text into context. Features add their own tables after the core ones.\nfunction ensureSchema(db: DatabaseSync, cfg: Config, tokenize: string): void {\n  db.exec(`CREATE TABLE IF NOT EXISTS frontmatter (\"path\" TEXT PRIMARY KEY, \"_mtime\" REAL, \"_ctime\" REAL, \"_size\" INTEGER, \"_parse_error\" TEXT)`);\n  // IF NOT EXISTS is safe against a tokenizer change: open() compares the table's own DDL\n  // against the resolved tokenizer before this runs, so a stale table is already gone by now.\n  // The three `_seg` sidecars are appended after path, never inserted: bm25(content, ...) and\n  // snippet(content, 2, ...) are documented against the first three columns and keep working\n  // (FTS5 defaults the weights it was not given). 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Features add their own tables after the core ones.\nfunction ensureSchema(db: DatabaseSync, cfg: Config, tokenize: string): void {\n  db.exec(`CREATE TABLE IF NOT EXISTS frontmatter (\"path\" TEXT PRIMARY KEY, \"_mtime\" REAL, \"_ctime\" REAL, \"_size\" INTEGER, \"_parse_error\" TEXT)`);\n  // IF NOT EXISTS is safe against a tokenizer change: open() compares the table's own DDL\n  // against the resolved tokenizer before this runs, so a stale table is already gone by now.\n  // The three `_seg` sidecars are appended after path, never inserted: bm25(content, ...) and\n  // snippet(content, 2, ...) are documented against the first three columns and keep working\n  // (FTS5 defaults the weights it was not given). Each carries its field's exploded unspaced\n  // runs for text that needs it, and an empty string for text that does not.\n  db.exec(`CREATE VIRTUAL TABLE IF NOT EXISTS content USING fts5(title, summary, text, path UNINDEXED, title_seg, summary_seg, text_seg, tokenize = '${tokenize}')`);\n  // Coverage, not ownership: a path can appear under several presets. path leads the PK so the\n  // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.\n  db.exec(`CREATE TABLE IF NOT EXISTS preset_files (\"path\" TEXT, preset TEXT, PRIMARY KEY (\"path\", preset))`);\n  db.exec('CREATE INDEX IF NOT EXISTS preset_files_preset ON preset_files(preset)');\n  for (const feature of activeFeatures(cfg)) feature.schema(db);\n  if (getMeta(db, 'schema_version') === null) setMeta(db, 'schema_version', SCHEMA_VERSION);\n  if (getMeta(db, 'features') === null) setMeta(db, 'features', featureSignature(cfg));\n}\n\nexport function docCount(db: DatabaseSync): number {\n  const row = db.prepare('SELECT COUNT(*) AS n FROM frontmatter').get() as { n: number };\n  return row.n;\n}\n\nexport function open(cfg: ResolvedConfig): OpenResult {\n  const stateDir = join(cfg.baseDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, DB_FILENAME);\n\n  const db = new DatabaseSync(dbPath);\n  db.exec('PRAGMA journal_mode = WAL');\n  // Covers a concurrent watcher's bulk reconcile (~5s for 500 files at 26k notes). A query\n  // that outwaits it still fails loudly.\n  db.exec('PRAGMA busy_timeout = 30000');\n  registerFunctions(db, contentTokenize(cfg) === undefined);\n\n  db.exec('CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT)');\n\n  // Before the rebuild branch below, never after: that branch deletes the cache, so a typo'd\n  // tokenizer validated later would cost a full re-index (and re-embed) to reach its own error.\n  const tokenize = resolveTokenize(db, cfg);\n\n  // Schema-version or feature-set mismatch: reconcile only reparses changed files, so an\n  // old cache can't be patched incrementally -- rebuild instead (cheap: nothing expensive lives here).\n  const version = getMeta(db, 'schema_version');\n  const features = getMeta(db, 'features');\n  const wantFeatures = featureSignature(cfg);\n  let tokenizeOnlyRebuild = false;\n  if ((version !== null && version !== SCHEMA_VERSION) || (features !== null && features !== wantFeatures)) {\n    // Indexing derives from presets, so a config edit rebuilding the cache must say so and\n    // name what changed -- silent rebuilds make derived indexing look like a hang or a bug.\n    if (version !== null && version !== SCHEMA_VERSION) {\n      console.error('sense: cache format changed (new sensemaking version); rebuilding the index');\n      db.close();\n      clearCache(cfg);\n      return open(cfg);\n    }\n    const changedKeys = changedSignatureKeys(features ?? '', wantFeatures);\n    // Only the tokenizer moved: frontmatter, links, sections, and embeddings are file-derived\n    // and tokenizer-independent, so they don't need re-deriving. Everything else -- a preset\n    // edit, an embed model change -- still takes the full clear/reopen below.\n    if (changedKeys.size === 1 && changedKeys.has('tokenize')) {\n      console.error('sense: config change (content tokenizer) rebuilds the text index; vectors, links, and sections are kept');\n      db.exec('DROP TABLE content');\n      tokenizeOnlyRebuild = true;\n    } else {\n      const changed = signatureDiff(features ?? '', wantFeatures);\n      console.error(`sense: config change (${changed}) rebuilds the index`);\n      db.close();\n      clearCache(cfg);\n      return open(cfg);\n    }\n  }\n\n  // Meta can lie after a crash between table creation and the signature write; the table's\n  // own DDL cannot. A mismatch here rebuilds no matter what meta says. A tokenize-only rebuild\n  // just dropped content above, so storedTokenize sees no table and this guard is skipped\n  // naturally rather than needing its own case.\n  const stored = storedTokenize(db);\n  if (stored !== null && stored !== tokenize) {\n    console.error('sense: cache was built with a different content tokenizer; rebuilding the index');\n    db.close();\n    clearCache(cfg);\n    return open(cfg);\n  }\n\n  ensureSchema(db, cfg, tokenize);\n\n  let rebuildWarnings: string[] = [];\n  if (tokenizeOnlyRebuild) {\n    rebuildWarnings = rebuildContentTable(db, cfg, cfg.baseDir);\n    setMeta(db, 'features', wantFeatures);\n  }\n\n  // 3x the largest reconcile this cache has recorded, floored at 30s and capped at 10min.\n  // Installed before reconcile() -- that call is the one that races a watcher's transaction.\n  const recordedMaxMs = Number(getMeta(db, 'reconcile_max_ms') ?? '0');\n  db.exec(`PRAGMA busy_timeout = ${Math.min(Math.max(30000, 3 * recordedMaxMs), 600_000)}`);\n\n  const { parsed, warnings } = reconcile(db, cfg, cfg.baseDir);\n\n  return { db, cfg, dbPath, parsed, warnings: [...rebuildWarnings, ...warnings] };\n}\n\n// Deletes the cache directory, and only that. The rebuild is not this function's job: the next\n// open() reconciles, which is what running any command already does, so a verb that bundled the\n// two described the half that was not its own. Manual reset for a doubted cache; the schema and\n// config-signature mismatches below reset themselves.\nexport function clearCache(cfg: ResolvedConfig): void {\n  rmSync(join(cfg.baseDir, STATE_DIR), { recursive: true, force: true });\n}\n"],"names":["mkdirSync","rmSync","join","DatabaseSync","contentTokenize","featureSignature","STATE_DIR","SenseError","activeFeatures","registerFunctions","changedSignatureKeys","rebuildContentTable","reconcile","signatureDiff","getMeta","setMeta","DB_FILENAME","SCHEMA_VERSION","DEFAULT_TOKENIZE","resolveTokenize","db","cfg","configured","undefined","literal","replace","exec","err","message","storedTokenize","row","prepare","get","m","sql","match","ensureSchema","tokenize","feature","schema","docCount","n","open","stateDir","baseDir","recursive","dbPath","version","features","wantFeatures","tokenizeOnlyRebuild","console","error","close","clearCache","changedKeys","size","has","changed","stored","rebuildWarnings","recordedMaxMs","Number","Math","min","max","parsed","warnings","force"],"mappings":"AAAA,+FAA+F;AAC/F,iGAAiG;AACjG,SAASA,SAAS,EAAEC,MAAM,QAAQ,UAAU;AAC5C,SAASC,IAAI,QAAQ,YAAY;AACjC,SAASC,YAAY,QAAQ,cAAc;AAE3C,SAASC,eAAe,EAAEC,gBAAgB,EAAEC,SAAS,QAAQ,qBAAqB;AAClF,SAASC,UAAU,QAAQ,eAAe;AAC1C,SAASC,cAAc,QAAQ,uBAAuB;AACtD,SAASC,iBAAiB,QAAQ,sBAAsB;AACxD,SAASC,oBAAoB,EAAEC,mBAAmB,EAAEC,SAAS,EAAEC,aAAa,QAAQ,iBAAiB;AACrG,SAASC,OAAO,EAAEC,OAAO,QAAQ,cAAc;AAE/C,OAAO,MAAMC,cAAc,WAAW;AACtC,sFAAsF;AACtF,iCAAiC;AACjC,OAAO,MAAMC,iBAAiB,KAAK;AAUnC,yFAAyF;AACzF,2FAA2F;AAC3F,4FAA4F;AAC5F,qCAAqC;AACrC,MAAMC,mBAAmB;AAEzB,wFAAwF;AACxF,6FAA6F;AAC7F,6FAA6F;AAC7F,6FAA6F;AAC7F,+DAA+D;AAC/D,SAASC,gBAAgBC,EAAgB,EAAEC,GAAW;IACpD,MAAMC,aAAalB,gBAAgBiB;IACnC,IAAIC,eAAeC,WAAW,OAAOL;IACrC,MAAMM,UAAUF,WAAWG,OAAO,CAAC,MAAM;IACzC,IAAI;QACFL,GAAGM,IAAI,CAAC;QACRN,GAAGM,IAAI,CAAC,CAAC,yEAAyE,EAAEF,QAAQ,EAAE,CAAC;QAC/FJ,GAAGM,IAAI,CAAC;IACV,EAAE,OAAOC,KAAK;QACZ,MAAM,IAAIpB,WAAW,kBAAkB,CAAC,kBAAkB,EAAEe,WAAW,0CAA0C,EAAE,AAACK,IAAcC,OAAO,CAAC,8FAA8F,CAAC;IAC3O;IACA,OAAOJ;AACT;AAEA,uFAAuF;AACvF,2FAA2F;AAC3F,SAASK,eAAeT,EAAgB;IACtC,MAAMU,MAAMV,GAAGW,OAAO,CAAC,CAAC,oDAAoD,CAAC,EAAEC,GAAG;IAClF,IAAI,CAACF,KAAK,OAAO;IACjB,MAAMG,IAAIH,IAAII,GAAG,CAACC,KAAK,CAAC;IACxB,OAAOF,IAAIA,CAAC,CAAC,EAAE,GAAG;AACpB;AAEA,2FAA2F;AAC3F,wFAAwF;AACxF,SAASG,aAAahB,EAAgB,EAAEC,GAAW,EAAEgB,QAAgB;IACnEjB,GAAGM,IAAI,CAAC,CAAC,oIAAoI,CAAC;IAC9I,wFAAwF;IACxF,4FAA4F;IAC5F,4FAA4F;IAC5F,2FAA2F;IAC3F,2FAA2F;IAC3F,2EAA2E;IAC3EN,GAAGM,IAAI,CAAC,CAAC,0IAA0I,EAAEW,SAAS,EAAE,CAAC;IACjK,6FAA6F;IAC7F,qFAAqF;IACrFjB,GAAGM,IAAI,CAAC,CAAC,gGAAgG,CAAC;IAC1GN,GAAGM,IAAI,CAAC;IACR,KAAK,MAAMY,WAAW9B,eAAea,KAAMiB,QAAQC,MAAM,CAACnB;IAC1D,IAAIN,QAAQM,IAAI,sBAAsB,MAAML,QAAQK,IAAI,kBAAkBH;IAC1E,IAAIH,QAAQM,IAAI,gBAAgB,MAAML,QAAQK,IAAI,YAAYf,iBAAiBgB;AACjF;AAEA,OAAO,SAASmB,SAASpB,EAAgB;IACvC,MAAMU,MAAMV,GAAGW,OAAO,CAAC,yCAAyCC,GAAG;IACnE,OAAOF,IAAIW,CAAC;AACd;AAEA,OAAO,SAASC,KAAKrB,GAAmB;QAwETP;IAvE7B,MAAM6B,WAAWzC,KAAKmB,IAAIuB,OAAO,EAAEtC;IACnCN,UAAU2C,UAAU;QAAEE,WAAW;IAAK;IACtC,MAAMC,SAAS5C,KAAKyC,UAAU3B;IAE9B,MAAMI,KAAK,IAAIjB,aAAa2C;IAC5B1B,GAAGM,IAAI,CAAC;IACR,yFAAyF;IACzF,uCAAuC;IACvCN,GAAGM,IAAI,CAAC;IACRjB,kBAAkBW,IAAIhB,gBAAgBiB,SAASE;IAE/CH,GAAGM,IAAI,CAAC;IAER,2FAA2F;IAC3F,8FAA8F;IAC9F,MAAMW,WAAWlB,gBAAgBC,IAAIC;IAErC,uFAAuF;IACvF,qGAAqG;IACrG,MAAM0B,UAAUjC,QAAQM,IAAI;IAC5B,MAAM4B,WAAWlC,QAAQM,IAAI;IAC7B,MAAM6B,eAAe5C,iBAAiBgB;IACtC,IAAI6B,sBAAsB;IAC1B,IAAI,AAACH,YAAY,QAAQA,YAAY9B,kBAAoB+B,aAAa,QAAQA,aAAaC,cAAe;QACxG,uFAAuF;QACvF,wFAAwF;QACxF,IAAIF,YAAY,QAAQA,YAAY9B,gBAAgB;YAClDkC,QAAQC,KAAK,CAAC;YACdhC,GAAGiC,KAAK;YACRC,WAAWjC;YACX,OAAOqB,KAAKrB;QACd;QACA,MAAMkC,cAAc7C,qBAAqBsC,qBAAAA,sBAAAA,WAAY,IAAIC;QACzD,0FAA0F;QAC1F,yFAAyF;QACzF,0EAA0E;QAC1E,IAAIM,YAAYC,IAAI,KAAK,KAAKD,YAAYE,GAAG,CAAC,aAAa;YACzDN,QAAQC,KAAK,CAAC;YACdhC,GAAGM,IAAI,CAAC;YACRwB,sBAAsB;QACxB,OAAO;YACL,MAAMQ,UAAU7C,cAAcmC,qBAAAA,sBAAAA,WAAY,IAAIC;YAC9CE,QAAQC,KAAK,CAAC,CAAC,sBAAsB,EAAEM,QAAQ,oBAAoB,CAAC;YACpEtC,GAAGiC,KAAK;YACRC,WAAWjC;YACX,OAAOqB,KAAKrB;QACd;IACF;IAEA,yFAAyF;IACzF,6FAA6F;IAC7F,wFAAwF;IACxF,8CAA8C;IAC9C,MAAMsC,SAAS9B,eAAeT;IAC9B,IAAIuC,WAAW,QAAQA,WAAWtB,UAAU;QAC1Cc,QAAQC,KAAK,CAAC;QACdhC,GAAGiC,KAAK;QACRC,WAAWjC;QACX,OAAOqB,KAAKrB;IACd;IAEAe,aAAahB,IAAIC,KAAKgB;IAEtB,IAAIuB,kBAA4B,EAAE;IAClC,IAAIV,qBAAqB;QACvBU,kBAAkBjD,oBAAoBS,IAAIC,KAAKA,IAAIuB,OAAO;QAC1D7B,QAAQK,IAAI,YAAY6B;IAC1B;IAEA,wFAAwF;IACxF,2FAA2F;IAC3F,MAAMY,gBAAgBC,QAAOhD,WAAAA,QAAQM,IAAI,iCAAZN,sBAAAA,WAAmC;IAChEM,GAAGM,IAAI,CAAC,CAAC,sBAAsB,EAAEqC,KAAKC,GAAG,CAACD,KAAKE,GAAG,CAAC,OAAO,IAAIJ,gBAAgB,SAAU;IAExF,MAAM,EAAEK,MAAM,EAAEC,QAAQ,EAAE,GAAGvD,UAAUQ,IAAIC,KAAKA,IAAIuB,OAAO;IAE3D,OAAO;QAAExB;QAAIC;QAAKyB;QAAQoB;QAAQC,UAAU;eAAIP;eAAoBO;SAAS;IAAC;AAChF;AAEA,+FAA+F;AAC/F,gGAAgG;AAChG,gGAAgG;AAChG,sDAAsD;AACtD,OAAO,SAASb,WAAWjC,GAAmB;IAC5CpB,OAAOC,KAAKmB,IAAIuB,OAAO,EAAEtC,YAAY;QAAEuC,WAAW;QAAMuB,OAAO;IAAK;AACtE"}

package/dist/esm/features/links.js

@@ -1,10 +1,23 @@
 import posix from 'node:path/posix';
+import { maskRegions } from '../fences.js';
 // links(src, target, target_base, dst, embed): target as written, target_base its baseKey
 // (indexed, for the incremental resolve below), dst the resolved path or NULL (a
 // queryable dead link), embed whether it's `![[x]]`/`![](x.md)` rather than `[[x]]`/`[](x.md)`
 // -- Obsidian's grain: a target both linked and embedded in the same note is two rows.
-// Wikilinks ([[target]], [[target#anchor|alias]], embeds) plus relative markdown links to .md files.
-function extract(_raw, body) {
+// 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) {
+    const beforeAlias = inner.split('|')[0].trim();
+    if (beforeAlias.startsWith('#')) return beforeAlias.length > 1 ? beforeAlias : null;
+    const target = beforeAlias.split('#')[0].trim();
+    return target || null;
+}
+function extract(_raw, rawBody, _search, data) {
+    const body = /\[\[|\]\(/.test(rawBody) ? maskRegions(rawBody) : rawBody;
     const seen = new Set();
     const results = [];
     const add = (target, embed)=>{
@@ -17,15 +30,37 @@ function extract(_raw, body) {
         });
     };
     // 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 (const m of body.matchAll(/\[\[(.*?)\]\]/g)){
         var _m_index;
-        const target = m[1].split('|')[0].split('#')[0].trim();
+        const target = parseWikilinkInner(m[1]);
         if (target) add(target, body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!');
     }
-    for (const m of body.matchAll(/(!)?\[[^\]]*\]\(([^)]+\.md)(?:#[^)]*)?\)/g)){
-        const target = m[2].trim();
-        if (target && !/^[a-z]+:\/\//i.test(target)) add(target, m[1] === '!');
+    // Any internal destination, not only .md-suffixed: Obsidian gives markdown links full
+    // linkpath resolution, so \](Zektor) resolves like [[Zektor]] and \](#anchor) is a
+    // self-edge. External URLs (a scheme anywhere survives the malformed double-paren case)
+    // and titled links (dest stops at whitespace) are skipped.
+    // A space in the destination is only valid ahead of a quoted title; a domain-shaped first
+    // segment (www.example.com/...) is external even without a scheme.
+    for (const m of body.matchAll(/(!)?\[[^\]]*\]\(((?:[^()\s]|\([^()\s]*\))+)(?:\s+(?:"[^)]*"|'[^)]*'))?\)/g)){
+        const dest = m[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 (/^([a-z][a-z0-9+.-]*:|\/\/|www\.)/i.test(dest)) continue;
+        const target = dest.startsWith('#') ? dest : dest.split('#')[0];
+        if (target) add(target, m[1] === '!');
+    }
+    for (const value of Object.values(data !== null && data !== void 0 ? data : {})){
+        for (const item of Array.isArray(value) ? value : [
+            value
+        ]){
+            if (typeof item !== 'string') continue;
+            const m = /^\[\[(.*)\]\]$/.exec(item.trim());
+            if (!m) continue;
+            const target = parseWikilinkInner(m[1]);
+            if (target) add(target, false);
+        }
     }
     return results;
 }
@@ -36,10 +71,11 @@ function baseKey(path) {
     return posix.basename(path).replace(/\.md$/i, '').toLowerCase();
 }
 // Obsidian-style: exact relative path (with/without .md), path relative to the linking
-// note's directory, then basename match (lexicographically first on ties).
+// note's directory, then basename match (shortest path wins on ties -- verified against a
+// cold-loaded Obsidian vault on 6+ real collision pairs; byBase's lists are pre-sorted that way).
 function resolveTarget(src, target, pathSet, byBase) {
-    var _ref;
-    var _byBase_get;
+    // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.
+    if (target.startsWith('#')) return src;
     const clean = cleanTarget(target);
     const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));
     for (const candidate of [
@@ -50,11 +86,18 @@ function resolveTarget(src, target, pathSet, byBase) {
     ]){
         if (pathSet.has(candidate)) return candidate;
     }
-    return (_ref = (_byBase_get = byBase.get(baseKey(clean))) === null || _byBase_get === void 0 ? void 0 : _byBase_get[0]) !== null && _ref !== void 0 ? _ref : null;
+    const candidates = byBase.get(baseKey(clean));
+    if (!candidates) return null;
+    // The linking note itself wins a basename collision (Obsidian resolves to self before the
+    // shortest-path rule -- cold-load verified on the hub corpus).
+    return candidates.includes(src) ? src : candidates[0];
 }
+// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own
+// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.
 function buildByBase(files) {
     const byBase = new Map();
-    for (const path of files.map((f)=>f.relPath).sort()){
+    const paths = files.map((f)=>f.relPath).sort((a, b)=>a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));
+    for (const path of paths){
         const key = baseKey(path);
         const list = byBase.get(key);
         if (list) list.push(path);
@@ -126,9 +169,12 @@ export function linkEdges(db) {
     // 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.
-    const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0
+    // 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
     UNION ALL
-    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1
+    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)=>[
             r.src,
@@ -188,7 +234,10 @@ export const links = {
         // 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');
-        for (const { target, embed } of targets)insert.run(path, target, baseKey(cleanTarget(target)), embed ? 1 : 0);
+        // 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;