sensemaking 0.15.0 → 0.15.1

package/dist/cjs/commands/peek.js

@@ -135,7 +135,7 @@ function peek(db, cfg, pathArg) {
     var backlinksTotal = 0;
     var _allowed = (0, _scopets.scopedPaths)(db, cfg, overrides);
     if ((0, _indexts.featureEnabled)(cfg, 'links')) {
-        var out = db.prepare('SELECT target, dst FROM links WHERE src = ? ORDER BY target').all(path);
+        var out = db.prepare('SELECT target, dst FROM links WHERE src = ? AND (dst IS NULL OR dst != src) ORDER BY target').all(path);
         outbound = _to_consumable_array(new Set(out.filter(function(l) {
             return l.dst !== null;
         }).map(function(l) {
@@ -146,8 +146,8 @@ function peek(db, cfg, pathArg) {
         }).map(function(l) {
             return 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(function(r) {
+        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(function(r) {
             return r.src;
         });
     }

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

@@ -1 +1 @@
-{"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\". Same reason `_parse_error` sits in the row.\n  parseError: string | null;\n  sections: Row[];\n  outbound: string[];\n  backlinks: string[];\n  unresolved: string[];\n  // Totals before truncation: a hub can have thousands of backlinks (or a note thousands of\n  // headings), and peek's whole point is bounded output. 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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\". Same reason `_parse_error` sits in the row.\n  parseError: string | null;\n  sections: Row[];\n  outbound: string[];\n  backlinks: string[];\n  unresolved: string[];\n  // Totals before truncation: a hub can have thousands of backlinks (or a note thousands of\n  // headings), and peek's whole point is bounded output. 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/cjs/commands/related.js

@@ -176,10 +176,10 @@ function relatedNotes(db, cfg, pathArg, overrides, k) {
                         return r.path;
                     });
                     path = (0, _peekts.resolveNote)(paths, pathArg);
-                    outbound = db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL').all(path).map(function(r) {
+                    outbound = db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? AND dst IS NOT NULL AND dst != src').all(path).map(function(r) {
                         return r.dst;
                     });
-                    backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ?').all(path).map(function(r) {
+                    backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? AND src != dst').all(path).map(function(r) {
                         return r.src;
                     });
                     exclude = new Set([

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

@@ -1 +1 @@
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+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/commands/related.ts"],"sourcesContent":["import type { DatabaseSync } from 'node:sqlite';\nimport type { ResolvedConfig, SearchOverrides } from '../config/index.ts';\nimport { embedEnabled, resolveSearch } from '../config/index.ts';\nimport { SenseError } from '../errors.ts';\nimport { embedPending, hasEmbedding, modelPresent, similarNotes } from '../features/embed.ts';\nimport { resolveNote } from './peek.ts';\nimport { scopedPaths, scopeHasEmbeddings } from './scope.ts';\n\n// Notes most similar by cosine, excluding self and everything already linked either way.\n// Its own command, not a peek section: a full embeddings scan is ~480ms at 26k notes.\nexport async function relatedNotes(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string, overrides: SearchOverrides, k: number): Promise<Array<{ path: string; similarity: number }>> {\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 outbound = (db.prepare('SELECT DISTINCT dst FROM links WHERE src = ? 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package/dist/cjs/db/open.d.cts

@@ -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/cjs/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/cjs/db/open.js

@@ -62,7 +62,7 @@ function _unsupported_iterable_to_array(o, minLen) {
     if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _array_like_to_array(o, minLen);
 }
 var DB_FILENAME = 'cache.db';
-var SCHEMA_VERSION = '15';
+var 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/cjs/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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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 = '${tokenize}')`);\n  // Coverage, not ownership: a path can appear under several presets. path leads the PK so the\n  // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.\n  db.exec(`CREATE TABLE IF NOT EXISTS preset_files (\"path\" TEXT, preset TEXT, PRIMARY KEY (\"path\", preset))`);\n  db.exec('CREATE INDEX IF NOT EXISTS preset_files_preset ON preset_files(preset)');\n  for (const feature of activeFeatures(cfg)) feature.schema(db);\n  if (getMeta(db, 'schema_version') === null) setMeta(db, 'schema_version', SCHEMA_VERSION);\n  if (getMeta(db, 'features') === null) setMeta(db, 'features', featureSignature(cfg));\n}\n\nexport function docCount(db: DatabaseSync): number {\n  const row = db.prepare('SELECT COUNT(*) AS n FROM frontmatter').get() as { n: number };\n  return row.n;\n}\n\nexport function open(cfg: ResolvedConfig): OpenResult {\n  const stateDir = join(cfg.baseDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, DB_FILENAME);\n\n  const db = new DatabaseSync(dbPath);\n  db.exec('PRAGMA journal_mode = WAL');\n  // Covers a concurrent watcher's bulk reconcile (~5s for 500 files at 26k notes). 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'', wantFeatures);\n    // Only the tokenizer moved: frontmatter, links, sections, and embeddings are file-derived\n    // and tokenizer-independent, so they don't need re-deriving. Everything else -- a preset\n    // edit, an embed model change -- still takes the full clear/reopen below.\n    if (changedKeys.size === 1 && changedKeys.has('tokenize')) {\n      console.error('sense: config change (content tokenizer) rebuilds the text index; vectors, links, and sections are kept');\n      db.exec('DROP TABLE content');\n      tokenizeOnlyRebuild = true;\n    } else {\n      const changed = signatureDiff(features ?? '', wantFeatures);\n      console.error(`sense: config change (${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. 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It means no table\n// of which version added which tokenizer has to be maintained.\nfunction resolveTokenize(db: DatabaseSync, cfg: Config): string {\n  const configured = contentTokenize(cfg);\n  if (configured === undefined) return DEFAULT_TOKENIZE;\n  const literal = configured.replace(/'/g, \"''\");\n  try {\n    db.exec('DROP TABLE IF EXISTS temp.sense_tokenize_probe');\n    db.exec(`CREATE VIRTUAL TABLE temp.sense_tokenize_probe USING fts5(x, tokenize = '${literal}')`);\n    db.exec('DROP TABLE IF EXISTS temp.sense_tokenize_probe');\n  } catch (err) {\n    throw new SenseError('CONFIG_INVALID', `content.tokenize \"${configured}\" is not a tokenizer this SQLite accepts (${(err as Error).message}); the built-in choices are unicode61, ascii, porter, and trigram, each with their own options`);\n  }\n  return literal;\n}\n\n// The tokenizer the content table was actually built with, from its own DDL -- the one\n// record that cannot desynchronize from the table. NULL when the table does not exist yet.\nfunction storedTokenize(db: DatabaseSync): string | null {\n  const row = db.prepare(`SELECT sql FROM sqlite_master WHERE name = 'content'`).get() as { sql: string } | undefined;\n  if (!row) return null;\n  const m = row.sql.match(/tokenize = '((?:[^']|'')*)'/);\n  return m ? m[1] : null;\n}\n\n// Content is a separate table (not a column on frontmatter) so `SELECT * FROM frontmatter`\n// can't dump file text into context. Features add their own tables after the core ones.\nfunction ensureSchema(db: DatabaseSync, cfg: Config, tokenize: string): void {\n  db.exec(`CREATE TABLE IF NOT EXISTS frontmatter (\"path\" TEXT PRIMARY KEY, \"_mtime\" REAL, \"_ctime\" REAL, \"_size\" INTEGER, \"_parse_error\" TEXT)`);\n  // IF NOT EXISTS is safe against a tokenizer change: open() compares the table's own DDL\n  // against the resolved tokenizer before this runs, so a stale table is already gone by now.\n  // The three `_seg` sidecars are appended after path, never inserted: bm25(content, ...) and\n  // snippet(content, 2, ...) are documented against the first three columns and keep working\n  // (FTS5 defaults the weights it was not given). Each carries its field's exploded unspaced\n  // runs for text that needs it, and an empty string for text that does not.\n  db.exec(`CREATE VIRTUAL TABLE IF NOT EXISTS content USING fts5(title, summary, text, path UNINDEXED, title_seg, summary_seg, text_seg, tokenize = '${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":["DB_FILENAME","SCHEMA_VERSION","clearCache","docCount","open","DEFAULT_TOKENIZE","resolveTokenize","db","cfg","configured","contentTokenize","undefined","literal","replace","exec","err","SenseError","message","storedTokenize","row","prepare","get","m","sql","match","ensureSchema","tokenize","activeFeatures","feature","schema","getMeta","setMeta","featureSignature","n","stateDir","join","baseDir","STATE_DIR","mkdirSync","recursive","dbPath","DatabaseSync","registerFunctions","version","features","wantFeatures","tokenizeOnlyRebuild","console","error","close","changedKeys","changedSignatureKeys","size","has","changed","signatureDiff","stored","rebuildWarnings","rebuildContentTable","recordedMaxMs","Number","Math","min","max","reconcile","parsed","warnings","rmSync","force"],"mappings":"AAAA,+FAA+F;AAC/F,iGAAiG;;;;;;;;;;;;QAYpFA;eAAAA;;QAGAC;eAAAA;;QAyJGC;eAAAA;;QAzFAC;eAAAA;;QAKAC;eAAAA;;;sBAnFkB;wBACb;0BACQ;uBAEgC;wBAClC;wBACI;8BACG;2BACkD;wBACnD;;;;;;;;;;;;;;;;;;;;;;;;;;AAE1B,IAAMJ,cAAc;AAGpB,IAAMC,iBAAiB;AAU9B,yFAAyF;AACzF,2FAA2F;AAC3F,4FAA4F;AAC5F,qCAAqC;AACrC,IAAMI,mBAAmB;AAEzB,wFAAwF;AACxF,6FAA6F;AAC7F,6FAA6F;AAC7F,6FAA6F;AAC7F,+DAA+D;AAC/D,SAASC,gBAAgBC,EAAgB,EAAEC,GAAW;IACpD,IAAMC,aAAaC,IAAAA,wBAAe,EAACF;IACnC,IAAIC,eAAeE,WAAW,OAAON;IACrC,IAAMO,UAAUH,WAAWI,OAAO,CAAC,MAAM;IACzC,IAAI;QACFN,GAAGO,IAAI,CAAC;QACRP,GAAGO,IAAI,CAAC,AAAC,4EAAmF,OAARF,SAAQ;QAC5FL,GAAGO,IAAI,CAAC;IACV,EAAE,OAAOC,KAAK;QACZ,MAAM,IAAIC,oBAAU,CAAC,kBAAkB,AAAC,qBAA2E,OAAvDP,YAAW,8CAAmE,OAAvB,AAACM,IAAcE,OAAO,EAAC;IAC5I;IACA,OAAOL;AACT;AAEA,uFAAuF;AACvF,2FAA2F;AAC3F,SAASM,eAAeX,EAAgB;IACtC,IAAMY,MAAMZ,GAAGa,OAAO,CAAC,wDAAwDC,GAAG;IAClF,IAAI,CAACF,KAAK,OAAO;IACjB,IAAMG,IAAIH,IAAII,GAAG,CAACC,KAAK,CAAC;IACxB,OAAOF,IAAIA,CAAC,CAAC,EAAE,GAAG;AACpB;AAEA,2FAA2F;AAC3F,wFAAwF;AACxF,SAASG,aAAalB,EAAgB,EAAEC,GAAW,EAAEkB,QAAgB;IACnEnB,GAAGO,IAAI,CAAC;IACR,wFAAwF;IACxF,4FAA4F;IAC5F,4FAA4F;IAC5F,2FAA2F;IAC3F,2FAA2F;IAC3F,2EAA2E;IAC3EP,GAAGO,IAAI,CAAC,AAAC,6IAAqJ,OAATY,UAAS;IAC9J,6FAA6F;IAC7F,qFAAqF;IACrFnB,GAAGO,IAAI,CAAC;IACRP,GAAGO,IAAI,CAAC;QACH,kCAAA,2BAAA;;QAAL,QAAK,YAAiBa,IAAAA,wBAAc,EAACnB,yBAAhC,SAAA,6BAAA,QAAA,yBAAA;YAAA,IAAMoB,UAAN;YAAsCA,QAAQC,MAAM,CAACtB;;;QAArD;QAAA;;;iBAAA,6BAAA;gBAAA;;;gBAAA;sBAAA;;;;IACL,IAAIuB,IAAAA,iBAAO,EAACvB,IAAI,sBAAsB,MAAMwB,IAAAA,iBAAO,EAACxB,IAAI,kBAAkBN;IAC1E,IAAI6B,IAAAA,iBAAO,EAACvB,IAAI,gBAAgB,MAAMwB,IAAAA,iBAAO,EAACxB,IAAI,YAAYyB,IAAAA,yBAAgB,EAACxB;AACjF;AAEO,SAASL,SAASI,EAAgB;IACvC,IAAMY,MAAMZ,GAAGa,OAAO,CAAC,yCAAyCC,GAAG;IACnE,OAAOF,IAAIc,CAAC;AACd;AAEO,SAAS7B,KAAKI,GAAmB;QAwETsB;IAvE7B,IAAMI,WAAWC,IAAAA,cAAI,EAAC3B,IAAI4B,OAAO,EAAEC,kBAAS;IAC5CC,IAAAA,iBAAS,EAACJ,UAAU;QAAEK,WAAW;IAAK;IACtC,IAAMC,SAASL,IAAAA,cAAI,EAACD,UAAUlC;IAE9B,IAAMO,KAAK,IAAIkC,wBAAY,CAACD;IAC5BjC,GAAGO,IAAI,CAAC;IACR,yFAAyF;IACzF,uCAAuC;IACvCP,GAAGO,IAAI,CAAC;IACR4B,IAAAA,iCAAiB,EAACnC,IAAIG,IAAAA,wBAAe,EAACF,SAASG;IAE/CJ,GAAGO,IAAI,CAAC;IAER,2FAA2F;IAC3F,8FAA8F;IAC9F,IAAMY,WAAWpB,gBAAgBC,IAAIC;IAErC,uFAAuF;IACvF,qGAAqG;IACrG,IAAMmC,UAAUb,IAAAA,iBAAO,EAACvB,IAAI;IAC5B,IAAMqC,WAAWd,IAAAA,iBAAO,EAACvB,IAAI;IAC7B,IAAMsC,eAAeb,IAAAA,yBAAgB,EAACxB;IACtC,IAAIsC,sBAAsB;IAC1B,IAAI,AAACH,YAAY,QAAQA,YAAY1C,kBAAoB2C,aAAa,QAAQA,aAAaC,cAAe;QACxG,uFAAuF;QACvF,wFAAwF;QACxF,IAAIF,YAAY,QAAQA,YAAY1C,gBAAgB;YAClD8C,QAAQC,KAAK,CAAC;YACdzC,GAAG0C,KAAK;YACR/C,WAAWM;YACX,OAAOJ,KAAKI;QACd;QACA,IAAM0C,cAAcC,IAAAA,iCAAoB,EAACP,qBAAAA,sBAAAA,WAAY,IAAIC;QACzD,0FAA0F;QAC1F,yFAAyF;QACzF,0EAA0E;QAC1E,IAAIK,YAAYE,IAAI,KAAK,KAAKF,YAAYG,GAAG,CAAC,aAAa;YACzDN,QAAQC,KAAK,CAAC;YACdzC,GAAGO,IAAI,CAAC;YACRgC,sBAAsB;QACxB,OAAO;YACL,IAAMQ,UAAUC,IAAAA,0BAAa,EAACX,qBAAAA,sBAAAA,WAAY,IAAIC;YAC9CE,QAAQC,KAAK,CAAC,AAAC,yBAAgC,OAARM,SAAQ;YAC/C/C,GAAG0C,KAAK;YACR/C,WAAWM;YACX,OAAOJ,KAAKI;QACd;IACF;IAEA,yFAAyF;IACzF,6FAA6F;IAC7F,wFAAwF;IACxF,8CAA8C;IAC9C,IAAMgD,SAAStC,eAAeX;IAC9B,IAAIiD,WAAW,QAAQA,WAAW9B,UAAU;QAC1CqB,QAAQC,KAAK,CAAC;QACdzC,GAAG0C,KAAK;QACR/C,WAAWM;QACX,OAAOJ,KAAKI;IACd;IAEAiB,aAAalB,IAAIC,KAAKkB;IAEtB,IAAI+B,kBAA4B,EAAE;IAClC,IAAIX,qBAAqB;QACvBW,kBAAkBC,IAAAA,gCAAmB,EAACnD,IAAIC,KAAKA,IAAI4B,OAAO;QAC1DL,IAAAA,iBAAO,EAACxB,IAAI,YAAYsC;IAC1B;IAEA,wFAAwF;IACxF,2FAA2F;IAC3F,IAAMc,gBAAgBC,QAAO9B,WAAAA,IAAAA,iBAAO,EAACvB,IAAI,iCAAZuB,sBAAAA,WAAmC;IAChEvB,GAAGO,IAAI,CAAC,AAAC,yBAA8E,OAAtD+C,KAAKC,GAAG,CAACD,KAAKE,GAAG,CAAC,OAAO,IAAIJ,gBAAgB;IAE9E,IAA6BK,aAAAA,IAAAA,sBAAS,EAACzD,IAAIC,KAAKA,IAAI4B,OAAO,GAAnD6B,SAAqBD,WAArBC,QAAQC,WAAaF,WAAbE;IAEhB,OAAO;QAAE3D,IAAAA;QAAIC,KAAAA;QAAKgC,QAAAA;QAAQyB,QAAAA;QAAQC,UAAU,AAAC,qBAAGT,wBAAiB,qBAAGS;IAAU;AAChF;AAMO,SAAShE,WAAWM,GAAmB;IAC5C2D,IAAAA,cAAM,EAAChC,IAAAA,cAAI,EAAC3B,IAAI4B,OAAO,EAAEC,kBAAS,GAAG;QAAEE,WAAW;QAAM6B,OAAO;IAAK;AACtE"}

package/dist/cjs/features/links.js

@@ -17,6 +17,7 @@ _export(exports, {
     }
 });
 var _posix = /*#__PURE__*/ _interop_require_default(require("node:path/posix"));
+var _fencests = require("../fences.js");
 function _array_like_to_array(arr, len) {
     if (len == null || len > arr.length) len = arr.length;
     for(var i = 0, arr2 = new Array(len); i < len; i++)arr2[i] = arr[i];
@@ -51,8 +52,11 @@ function _unsupported_iterable_to_array(o, minLen) {
 // (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).
+function extract(_raw, rawBody, _search, data) {
+    var body = /\[\[|\]\(/.test(rawBody) ? (0, _fencests.maskRegions)(rawBody) : rawBody;
     var seen = new Set();
     var results = [];
     var add = function add(target, embed) {
@@ -71,8 +75,16 @@ function extract(_raw, body) {
         for(var _iterator = body.matchAll(/\[\[(.*?)\]\]/g)[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
             var m = _step.value;
             var _m_index;
-            var target = m[1].split('|')[0].split('#')[0].trim();
-            if (target) add(target, body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!');
+            var embed = body[((_m_index = m.index) !== null && _m_index !== void 0 ? _m_index : 0) - 1] === '!';
+            // [[#Heading]]: a same-note anchor link, which Obsidian resolves to a self-edge. Keep the
+            // target as written (leading #) so resolveTarget can special-case it.
+            var beforeAlias = m[1].split('|')[0].trim();
+            if (beforeAlias.startsWith('#')) {
+                if (beforeAlias.length > 1) add(beforeAlias, embed);
+                continue;
+            }
+            var target = beforeAlias.split('#')[0].trim();
+            if (target) add(target, embed);
         }
     } catch (err) {
         _didIteratorError = true;
@@ -90,10 +102,19 @@ function extract(_raw, body) {
     }
     var _iteratorNormalCompletion1 = true, _didIteratorError1 = false, _iteratorError1 = undefined;
     try {
-        for(var _iterator1 = body.matchAll(/(!)?\[[^\]]*\]\(([^)]+\.md)(?:#[^)]*)?\)/g)[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
+        // 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(var _iterator1 = body.matchAll(/(!)?\[[^\]]*\]\(((?:[^()\s]|\([^()\s]*\))+)(?:\s+(?:"[^)]*"|'[^)]*'))?\)/g)[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
             var m1 = _step1.value;
-            var target1 = m1[2].trim();
-            if (target1 && !/^[a-z]+:\/\//i.test(target1)) add(target1, m1[1] === '!');
+            var dest = m1[2].trim();
+            if (!dest || dest.includes('://')) continue;
+            if (/^www\./i.test(dest)) continue;
+            var target1 = dest.startsWith('#') ? dest : dest.split('#')[0];
+            if (target1) add(target1, m1[1] === '!');
         }
     } catch (err) {
         _didIteratorError1 = true;
@@ -109,6 +130,53 @@ function extract(_raw, body) {
             }
         }
     }
+    var _iteratorNormalCompletion2 = true, _didIteratorError2 = false, _iteratorError2 = undefined;
+    try {
+        for(var _iterator2 = Object.values(data !== null && data !== void 0 ? data : {})[Symbol.iterator](), _step2; !(_iteratorNormalCompletion2 = (_step2 = _iterator2.next()).done); _iteratorNormalCompletion2 = true){
+            var value = _step2.value;
+            var _iteratorNormalCompletion3 = true, _didIteratorError3 = false, _iteratorError3 = undefined;
+            try {
+                for(var _iterator3 = (Array.isArray(value) ? value : [
+                    value
+                ])[Symbol.iterator](), _step3; !(_iteratorNormalCompletion3 = (_step3 = _iterator3.next()).done); _iteratorNormalCompletion3 = true){
+                    var item = _step3.value;
+                    if (typeof item !== 'string') continue;
+                    var m2 = /^\[\[(.*)\]\]$/.exec(item.trim());
+                    if (!m2) continue;
+                    var inner = m2[1].split('|')[0].trim();
+                    var target2 = inner.split('#')[0].trim();
+                    if (target2) add(target2, false);
+                    else if (inner.startsWith('#') && inner.length > 1) add(inner, false);
+                }
+            } catch (err) {
+                _didIteratorError3 = true;
+                _iteratorError3 = err;
+            } finally{
+                try {
+                    if (!_iteratorNormalCompletion3 && _iterator3.return != null) {
+                        _iterator3.return();
+                    }
+                } finally{
+                    if (_didIteratorError3) {
+                        throw _iteratorError3;
+                    }
+                }
+            }
+        }
+    } catch (err) {
+        _didIteratorError2 = true;
+        _iteratorError2 = err;
+    } finally{
+        try {
+            if (!_iteratorNormalCompletion2 && _iterator2.return != null) {
+                _iterator2.return();
+            }
+        } finally{
+            if (_didIteratorError2) {
+                throw _iteratorError2;
+            }
+        }
+    }
     return results;
 }
 function cleanTarget(target) {
@@ -118,10 +186,11 @@ function baseKey(path) {
     return _posix.default.basename(path).replace(/\.md$/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;
     var clean = cleanTarget(target);
     var fromSrc = _posix.default.normalize(_posix.default.join(_posix.default.dirname(src), clean));
     for(var _i = 0, _iter = [
@@ -133,15 +202,24 @@ function resolveTarget(src, target, pathSet, byBase) {
         var candidate = _iter[_i];
         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;
+    var 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) {
     var byBase = new Map();
+    var paths = files.map(function(f) {
+        return f.relPath;
+    }).sort(function(a, b) {
+        return a.length - b.length || (a < b ? -1 : a > b ? 1 : 0);
+    });
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
-        for(var _iterator = files.map(function(f) {
-            return f.relPath;
-        }).sort()[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
+        for(var _iterator = paths[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
             var path = _step.value;
             var key = baseKey(path);
             var list = byBase.get(key);
@@ -304,7 +382,10 @@ 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.
-    var sql = "SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.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.
+    var 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)";
     return db.prepare(sql).all().map(function(r) {
         return [
             r.src,
@@ -374,9 +455,12 @@ var links = {
         var 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');
         var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
         try {
+            // 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(var _iterator = targets[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
                 var _step_value = _step.value, target = _step_value.target, embed = _step_value.embed;
-                insert.run(path, target, baseKey(cleanTarget(target)), embed ? 1 : 0);
+                insert.run(path, target, target.startsWith('#') ? null : baseKey(cleanTarget(target)), embed ? 1 : 0);
             }
         } catch (err) {
             _didIteratorError = true;

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

@@ -1 +1 @@
-{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/features/links.ts"],"sourcesContent":["import posix from 'node:path/posix';\nimport type { DatabaseSync } from 'node:sqlite';\nimport type { FileStat } from '../scan.ts';\nimport type { Feature, ReconcileDelta } from './types.ts';\n\n// links(src, target, target_base, dst, embed): target as written, target_base its baseKey\n// (indexed, for the incremental resolve below), dst the resolved path or NULL (a\n// queryable dead link), embed whether it's `![[x]]`/`![](x.md)` rather than `[[x]]`/`[](x.md)`\n// -- Obsidian's grain: a target both linked and embedded in the same note is two rows.\n\n// Wikilinks ([[target]], [[target#anchor|alias]], embeds) plus relative markdown links to .md files.\nfunction extract(_raw: string, body: string): Array<{ target: string; embed: boolean }> {\n  const seen = new Set<string>();\n  const results: Array<{ target: string; embed: boolean }> = [];\n  const add = (target: string, embed: boolean) => {\n    const key = `${target}\\0${embed ? '1' : '0'}`;\n    if (seen.has(key)) return;\n    seen.add(key);\n    results.push({ target, embed });\n  };\n  // To the first ]], as Obsidian parses it, so a heading or alias holding a lone ] still\n  // matches; anchor and alias split off in code, since a class-based regex stops at the ].\n  for (const m of body.matchAll(/\\[\\[(.*?)\\]\\]/g)) {\n    const target = m[1].split('|')[0].split('#')[0].trim();\n    if (target) add(target, body[(m.index ?? 0) - 1] === '!');\n  }\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(([^)]+\\.md)(?:#[^)]*)?\\)/g)) {\n    const target = m[2].trim();\n    if (target && !/^[a-z]+:\\/\\//i.test(target)) add(target, m[1] === '!');\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$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking\n// note's directory, then basename match (lexicographically first on ties).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  return byBase.get(baseKey(clean))?.[0] ?? null;\n}\n\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  for (const path of files.map((f) => f.relPath).sort()) {\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  const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;\n  return (db.prepare(sql).all() as Array<{ src: string; dst: string }>).map((r) => [r.src, r.dst]);\n}\n\n// remove() has already deleted the rows by the time afterReconcile runs, so it records here\n// whether they carried edges. Keyed on the delta object, so the state dies with the reconcile.\nconst removedWithLinks = new WeakMap<ReconcileDelta, Set<string>>();\n\nfunction recordRemoved(delta: ReconcileDelta, path: string): void {\n  let set = removedWithLinks.get(delta);\n  if (!set) {\n    set = new Set();\n    removedWithLinks.set(delta, set);\n  }\n  set.add(path);\n}\n\n// remove() runs per path; the vanished list is an array, so cache the Set per delta.\nconst vanishedSets = new WeakMap<ReconcileDelta, Set<string>>();\nfunction vanishedSet(delta: ReconcileDelta): Set<string> {\n  let set = vanishedSets.get(delta);\n  if (!set) {\n    set = new Set(delta.vanished);\n    vanishedSets.set(delta, set);\n  }\n  return set;\n}\n\nexport const links: Feature = {\n  name: 'links',\n  schema(db) {\n    db.exec('CREATE TABLE IF NOT EXISTS links (src TEXT, target TEXT, target_base TEXT, dst TEXT, embed INTEGER, PRIMARY KEY (src, target, embed))');\n    db.exec('CREATE INDEX IF NOT EXISTS links_dst ON links(dst)');\n    db.exec('CREATE INDEX IF NOT EXISTS links_target_base ON links(target_base)');\n  },\n  extract,\n  // Reparsed docs are diffed in store() below instead of wiped here: deleting and\n  // re-inserting resets dst to NULL, which made every touch-only reparse read as an edge\n  // change and recompute PageRank -- measured as most of the remaining update cost.\n  remove(db, path, delta) {\n    if (!vanishedSet(delta).has(path)) return;\n    const result = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    if (Number(result.changes) > 0) recordRemoved(delta, path);\n  },\n  store(db, path, extracted, delta) {\n    const targets = extracted as Array<{ target: string; embed: boolean }>;\n    // Stale rows (target/embed pairs the new parse no longer contains) are real edge removals.\n    // \\0 can't appear in a target, so the composite key never collides.\n    let stale: ReturnType<ReturnType<DatabaseSync['prepare']>['run']>;\n    if (targets.length === 0) {\n      stale = db.prepare('DELETE FROM links WHERE src = ?').run(path);\n    } else {\n      const placeholders = targets.map(() => '?').join(', ');\n      const keys = targets.map((t) => `${t.target}\\0${t.embed ? '1' : '0'}`);\n      stale = db.prepare(`DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (${placeholders})`).run(path, ...keys);\n    }\n    if (Number(stale.changes) > 0) recordRemoved(delta, path);\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same\n    // value and reports no change; only genuinely new rows start at NULL.\n    const insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) 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Keep the\n    // target as written (leading #) so resolveTarget can special-case it.\n    const beforeAlias = m[1].split('|')[0].trim();\n    if (beforeAlias.startsWith('#')) {\n      if (beforeAlias.length > 1) add(beforeAlias, embed);\n      continue;\n    }\n    const target = beforeAlias.split('#')[0].trim();\n    if (target) add(target, embed);\n  }\n  // Any internal destination, not only .md-suffixed: Obsidian gives markdown links full\n  // linkpath resolution, so \\](Zektor) resolves like [[Zektor]] and \\](#anchor) is a\n  // self-edge. External URLs (a scheme anywhere survives the malformed double-paren case)\n  // and titled links (dest stops at whitespace) are skipped.\n  // A space in the destination is only valid ahead of a quoted title; a domain-shaped first\n  // segment (www.example.com/...) is external even without a scheme.\n  for (const m of body.matchAll(/(!)?\\[[^\\]]*\\]\\(((?:[^()\\s]|\\([^()\\s]*\\))+)(?:\\s+(?:\"[^)]*\"|'[^)]*'))?\\)/g)) {\n    const dest = m[2].trim();\n    if (!dest || dest.includes('://')) continue;\n    if (/^www\\./i.test(dest)) continue;\n    const target = dest.startsWith('#') ? dest : dest.split('#')[0];\n    if (target) add(target, m[1] === '!');\n  }\n  for (const value of Object.values(data ?? {})) {\n    for (const item of Array.isArray(value) ? value : [value]) {\n      if (typeof item !== 'string') continue;\n      const m = /^\\[\\[(.*)\\]\\]$/.exec(item.trim());\n      if (!m) continue;\n      const inner = m[1].split('|')[0].trim();\n      const target = inner.split('#')[0].trim();\n      if (target) add(target, false);\n      else if (inner.startsWith('#') && inner.length > 1) add(inner, false);\n    }\n  }\n  return results;\n}\n\nfunction cleanTarget(target: string): string {\n  return target.replace(/\\\\/g, '/').replace(/^\\.\\//, '');\n}\n\nfunction baseKey(path: string): string {\n  return posix.basename(path).replace(/\\.md$/i, '').toLowerCase();\n}\n\n// Obsidian-style: exact relative path (with/without .md), path relative to the linking\n// note's directory, then basename match (shortest path wins on ties -- verified against a\n// cold-loaded Obsidian vault on 6+ real collision pairs; byBase's lists are pre-sorted that way).\nfunction resolveTarget(src: string, target: string, pathSet: Set<string>, byBase: Map<string, string[]>): string | null {\n  // [[#Heading]]: a same-note anchor, always the note itself -- never depends on other files.\n  if (target.startsWith('#')) return src;\n  const clean = cleanTarget(target);\n  const fromSrc = posix.normalize(posix.join(posix.dirname(src), clean));\n  for (const candidate of [clean, `${clean}.md`, fromSrc, `${fromSrc}.md`]) {\n    if (pathSet.has(candidate)) return candidate;\n  }\n  const candidates = byBase.get(baseKey(clean));\n  if (!candidates) return null;\n  // The linking note itself wins a basename collision (Obsidian resolves to self before the\n  // shortest-path rule -- cold-load verified on the hub corpus).\n  return candidates.includes(src) ? src : candidates[0];\n}\n\n// Shortest path wins a basename collision; equal lengths fall back to lexicographic, our own\n// deterministic tiebreak for a case Obsidian itself leaves registration-order-dependent.\nfunction buildByBase(files: FileStat[]): Map<string, string[]> {\n  const byBase = new Map<string, string[]>();\n  const paths = files.map((f) => f.relPath).sort((a, b) => a.length - b.length || (a < b ? -1 : a > b ? 1 : 0));\n  for (const path of paths) {\n    const key = baseKey(path);\n    const list = byBase.get(key);\n    if (list) list.push(path);\n    else byBase.set(key, [path]);\n  }\n  return byBase;\n}\n\ninterface LinkRow {\n  src: string;\n  target: string;\n  dst: string | null;\n  embed: number;\n}\n\n// Applies resolveTarget to `rows`, writing only rows whose dst actually changes. The UPDATE\n// keys on (src, target): a link/embed sibling pair shares one resolution, so either row's\n// mismatch rewrites both.\nfunction resolveRows(db: DatabaseSync, rows: LinkRow[], pathSet: Set<string>, byBase: Map<string, string[]>): boolean {\n  const update = db.prepare('UPDATE links SET dst = ? WHERE src = ? 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package/dist/cjs/features/tags.js

@@ -161,53 +161,12 @@ function frontmatterTags(data) {
     }
     return found;
 }
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-// shorter or longer run in between is literal text, not a delimiter (CommonMark code spans).
-// Masked with spaces so column positions and tag-boundary whitespace are unaffected.
-function maskCodeSpans(line) {
-    var out = '';
-    var i = 0;
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-        if (line[i] !== '`') {
-            out += line[i];
-            i++;
-            continue;
-        }
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-            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;
-}
 // #tag tokens outside fenced code blocks, inline code spans, wikilinks, HTML tags, HTML blocks,
-// and link destinations.
+// <!-- --> comments, and link destinations.
 function inlineTags(body) {
     var found = [];
     var fence = (0, _fencests.fenceTracker)();
+    var comment = (0, _fencests.commentTracker)();
     var inHtmlBlock = false;
     var htmlBlockClose = null; // set while inside a type-1 (script/pre/style/textarea) block
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
@@ -226,11 +185,17 @@ function inlineTags(body) {
                 }
                 continue;
             }
-            if (fence.feed(line)) continue;
-            if (fence.inFence) continue;
+            if (!comment.inComment) {
+                if (fence.feed(line)) continue;
+                if (fence.inFence) continue;
+            }
+            // Obsidian parses nothing inside a <!-- --> comment; mask its span (which may open, close,
+            // or run the whole line) before any other check sees this line's text. Skipped when there
+            // is no comment marker anywhere near this line -- most lines, so worth the branch.
+            var masked = comment.inComment || line.includes('<!--') ? comment.mask(line) : line;
             // Indented or blockquoted HTML blocks still swallow their content in Obsidian, so the
             // opener test runs after stripping leading whitespace and > markers.
-            var stripped = line.replace(/^[ \t>]*/, '');
+            var stripped = masked.replace(/^[ \t>]*/, '');
             if (stripped[0] === '<') {
                 var openMatch = HTML_BLOCK_OPEN_RE.exec(stripped);
                 if (openMatch) {
@@ -248,8 +213,8 @@ function inlineTags(body) {
                     }
                 }
             }
-            if (!line.includes('#')) continue; // most lines; skip the regex work
-            var cleaned = line.includes('`') ? maskCodeSpans(line) : line;
+            if (!masked.includes('#')) continue; // most lines; skip the regex work
+            var cleaned = masked.includes('`') ? (0, _fencests.maskCodeSpans)(masked) : masked;
             if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, function(m) {
                 return ' '.repeat(m.length);
             });