sensemaking 0.13.1 → 0.14.0

package/dist/cjs/cli/shared.js

@@ -47,6 +47,7 @@ _export(exports, {
     }
 });
 var _nodeutil = require("node:util");
+var _columnhintts = require("../column-hint.js");
 var _indexts = require("../config/index.js");
 var _indexts1 = require("../db/index.js");
 var _outputts = require("../output.js");
@@ -466,12 +467,13 @@ function runSql(cfg, sql, params, format, label, preset) {
         });
         (0, _outputts.printRowStream)((_statement = statement).iterate.apply(_statement, _to_consumable_array(params)), format, columns);
     } catch (err) {
+        var hinted = (0, _columnhintts.columnHint)(db, err); // pragma needs the db still open
         db.close();
         // A saved query or ad-hoc SQL can carry `content MATCH ?` too, so the same FTS5
         // punctuation trap applies -- the bound parameters are the search terms there. SQL
         // without MATCH gets its error verbatim; search advice on a plain typo would mislead.
-        if (/\bMATCH\b/i.test(sql)) throw (0, _searcherrorts.searchError)(err, params.join(' '));
-        throw err;
+        if (/\bMATCH\b/i.test(sql)) throw (0, _searcherrorts.searchError)(hinted, params.join(' '));
+        throw hinted;
     }
     db.close();
 }

package/dist/cjs/cli/shared.js.map

@@ -1 +1 @@
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package/dist/cjs/column-hint.d.cts

@@ -0,0 +1,2 @@
+import type { DatabaseSync } from 'node:sqlite';
+export declare function columnHint(db: DatabaseSync, err: Error): Error;

package/dist/cjs/column-hint.d.ts

@@ -0,0 +1,2 @@
+import type { DatabaseSync } from 'node:sqlite';
+export declare function columnHint(db: DatabaseSync, err: Error): Error;

package/dist/cjs/column-hint.js

@@ -0,0 +1,104 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", {
+    value: true
+});
+Object.defineProperty(exports, "columnHint", {
+    enumerable: true,
+    get: function() {
+        return columnHint;
+    }
+});
+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];
+    return arr2;
+}
+function _array_without_holes(arr) {
+    if (Array.isArray(arr)) return _array_like_to_array(arr);
+}
+function _iterable_to_array(iter) {
+    if (typeof Symbol !== "undefined" && iter[Symbol.iterator] != null || iter["@@iterator"] != null) return Array.from(iter);
+}
+function _non_iterable_spread() {
+    throw new TypeError("Invalid attempt to spread non-iterable instance.\\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.");
+}
+function _to_consumable_array(arr) {
+    return _array_without_holes(arr) || _iterable_to_array(arr) || _unsupported_iterable_to_array(arr) || _non_iterable_spread();
+}
+function _unsupported_iterable_to_array(o, minLen) {
+    if (!o) return;
+    if (typeof o === "string") return _array_like_to_array(o, minLen);
+    var n = Object.prototype.toString.call(o).slice(8, -1);
+    if (n === "Object" && o.constructor) n = o.constructor.name;
+    if (n === "Map" || n === "Set") return Array.from(n);
+    if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _array_like_to_array(o, minLen);
+}
+// A frontmatter key with punctuation (`plugin-id`, `a.b`) is a real column, but naming it
+// unquoted in SQL parses as an expression: `plugin-id` is `plugin - id`, and SQLite's error
+// names a fragment (`plugin`) the user never wrote. This maps that fragment back to the
+// columns it could have come from, so the error names the actual fix instead.
+function startsWithBoundary(name, prefix) {
+    return name.length > prefix.length && name.startsWith(prefix) && /\W/.test(name[prefix.length]);
+}
+function columnHint(db, err) {
+    var match = /no such column: (\S+)/.exec(err.message);
+    if (!match) return err;
+    var token = match[1];
+    // `f.plugin` -> `plugin`; left as-is when there's no leading alias segment, which also
+    // covers a column literally named `a.b` -- the full-token check below matches that case
+    // directly, so stripping here never needs to special-case it.
+    var aliasStripped = token.replace(/^[A-Za-z_]\w*\./, '');
+    var forms = new Set([
+        token,
+        aliasStripped
+    ]);
+    var columns = db.prepare('PRAGMA table_info(frontmatter)').all().map(function(c) {
+        return c.name;
+    });
+    var candidates = new Set();
+    var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
+    try {
+        for(var _iterator = columns[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
+            var name = _step.value;
+            var _iteratorNormalCompletion1 = true, _didIteratorError1 = false, _iteratorError1 = undefined;
+            try {
+                for(var _iterator1 = forms[Symbol.iterator](), _step1; !(_iteratorNormalCompletion1 = (_step1 = _iterator1.next()).done); _iteratorNormalCompletion1 = true){
+                    var form = _step1.value;
+                    if (name === form || startsWithBoundary(name, form)) candidates.add(name);
+                }
+            } catch (err) {
+                _didIteratorError1 = true;
+                _iteratorError1 = err;
+            } finally{
+                try {
+                    if (!_iteratorNormalCompletion1 && _iterator1.return != null) {
+                        _iterator1.return();
+                    }
+                } finally{
+                    if (_didIteratorError1) {
+                        throw _iteratorError1;
+                    }
+                }
+            }
+        }
+    } catch (err) {
+        _didIteratorError = true;
+        _iteratorError = err;
+    } finally{
+        try {
+            if (!_iteratorNormalCompletion && _iterator.return != null) {
+                _iterator.return();
+            }
+        } finally{
+            if (_didIteratorError) {
+                throw _iteratorError;
+            }
+        }
+    }
+    if (candidates.size === 0) return err;
+    var quoted = _to_consumable_array(candidates).map(function(name) {
+        return '"'.concat(name.split('"').join('""'), '"');
+    }).join(', ');
+    return new Error("".concat(err.message, " -- ").concat(quoted, " needs double quotes in SQL: unquoted, SQLite parses the punctuation as an operator instead of column syntax."));
+}
+/* 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/column-hint.js.map

@@ -0,0 +1 @@
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package/dist/cjs/commands/scope.js

@@ -35,6 +35,7 @@ _export(exports, {
     }
 });
 var _nodepath = require("node:path");
+var _columnhintts = require("../column-hint.js");
 var _indexts = require("../config/index.js");
 function _array_like_to_array(arr, len) {
     if (len == null || len > arr.length) len = arr.length;
@@ -101,7 +102,12 @@ function rawScope(db, cfg, overrides, allPaths) {
 }
 function narrowByWhere(db, paths, where) {
     if (!where) return paths;
-    var whereRows = db.prepare('SELECT "path" FROM frontmatter f WHERE ('.concat(where, ")")).all();
+    var whereRows;
+    try {
+        whereRows = db.prepare('SELECT "path" FROM frontmatter f WHERE ('.concat(where, ")")).all();
+    } catch (err) {
+        throw (0, _columnhintts.columnHint)(db, err);
+    }
     var wherePaths = new Set(whereRows.map(function(r) {
         return r.path;
     }));

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

@@ -1 +1 @@
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Shared by scopedPaths() and search(), which also needs the\n// pre-where set to size the candidate-pool filter.\nexport function rawScope(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides, allPaths?: string[]): Set<string> {\n  const effective = resolveSearch(cfg, overrides);\n  const { include, exclude } = effective;\n  const adHocScope = overrides.include !== undefined || overrides.exclude !== undefined || overrides.noExclude === true;\n  if (!adHocScope) return new Set((db.prepare('SELECT \"path\" FROM preset_files WHERE preset = ?').all(effective.presetName) as Array<{ path: string }>).map((r) => r.path));\n  const paths = allPaths ?? 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(db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n  return new Set(paths.filter((p) => inScope(p, include, exclude)));\n}\n\nexport function narrowByWhere(db: DatabaseSync, paths: Set<string>, where: string | undefined): Set<string> {\n  if (!where) return paths;\n  let whereRows: Array<{ path: string }>;\n  try {\n    whereRows = db.prepare(`SELECT \"path\" FROM frontmatter f WHERE (${where})`).all() as Array<{ path: string }>;\n  } catch (err) {\n    throw columnHint(db, err as Error);\n  }\n  const wherePaths = new Set(whereRows.map((r) => r.path));\n  return new Set([...paths].filter((p) => wherePaths.has(p)));\n}\n\n// The scope resolver for non-search commands (path, peek, map): same coverage rule search()\n// applies, then narrowed by the resolved `where`.\nexport function scopedPaths(db: DatabaseSync, cfg: ResolvedConfig, overrides: SearchOverrides): Set<string> {\n  const effective = resolveSearch(cfg, overrides);\n  return narrowByWhere(db, rawScope(db, cfg, overrides), effective.where);\n}\n\n// Materializes a path set into a named temp table (same shape as traverse.ts's allowed_nodes)\n// so a query can join/filter against it cheaply instead of binding a parameter per path.\nexport function materializeScope(db: DatabaseSync, table: string, paths: Set<string>): void {\n  db.exec(`DROP TABLE IF EXISTS ${table}`);\n  db.exec(`CREATE TEMP TABLE ${table} (\"path\" TEXT PRIMARY KEY)`);\n  db.prepare(`INSERT INTO ${table} SELECT DISTINCT value FROM json_each(?1)`).run(JSON.stringify([...paths]));\n}\n\nexport function setupMapScope(db: DatabaseSync, paths: Set<string>): void {\n  materializeScope(db, '_map_scope', paths);\n}\n"],"names":["INTERNAL_COLUMNS","inScope","materializeScope","narrowByWhere","rawScope","scopeHasEmbeddings","scopedPaths","setupMapScope","Set","path","include","exclude","some","g","matchesGlob","db","cfg","anyPresetEmbeds","rows","prepare","all","r","has","overrides","allPaths","effective","resolveSearch","adHocScope","undefined","noExclude","presetName","map","paths","filter","p","where","whereRows","err","columnHint","wherePaths","table","exec","run","JSON","stringify"],"mappings":";;;;;;;;;;;QAMaA;eAAAA;;QAKGC;eAAAA;;QA6CAC;eAAAA;;QArBAC;eAAAA;;QATAC;eAAAA;;QATAC;eAAAA;;QAgCAC;eAAAA;;QAaAC;eAAAA;;;wBA9DY;4BAED;uBAEoB;;;;;;;;;;;;;;;;;;;;;;;;;;AAExC,IAAMP,mBAAmB,IAAIQ,IAAI;IAAC;IAAQ;IAAU;IAAU;IAAS;IAAS;CAAe;AAK/F,SAASP,QAAQQ,IAAY,EAAEC,OAAiB,EAAEC,OAAkB;IACzE,IAAI,CAACD,QAAQE,IAAI,CAAC,SAACC;eAAMC,IAAAA,qBAAW,EAACL,MAAMI;QAAK,OAAO;IACvD,IAAIF,oBAAAA,8BAAAA,QAASC,IAAI,CAAC,SAACC;eAAMC,IAAAA,qBAAW,EAACL,MAAMI;QAAK,OAAO;IACvD,OAAO;AACT;AAEO,SAASR,mBAAmBU,EAAgB,EAAEC,GAAmB,EAAEV,WAAwB;IAChG,IAAI,CAACW,IAAAA,wBAAe,EAACD,MAAM,OAAO,OAAO,yDAAyD;IAClG,IAAME,OAAOH,GAAGI,OAAO,CAAC,0CAA0CC,GAAG;IACrE,OAAOF,KAAKN,IAAI,CAAC,SAACS;eAAMf,YAAYgB,GAAG,CAACD,EAAEZ,IAAI;;AAChD;AAKO,SAASL,SAASW,EAAgB,EAAEC,GAAmB,EAAEO,SAA0B,EAAEC,QAAmB;IAC7G,IAAMC,YAAYC,IAAAA,sBAAa,EAACV,KAAKO;IACrC,IAAQb,UAAqBe,UAArBf,SAASC,UAAYc,UAAZd;IACjB,IAAMgB,aAAaJ,UAAUb,OAAO,KAAKkB,aAAaL,UAAUZ,OAAO,KAAKiB,aAAaL,UAAUM,SAAS,KAAK;IACjH,IAAI,CAACF,YAAY,OAAO,IAAInB,IAAI,AAACO,GAAGI,OAAO,CAAC,oDAAoDC,GAAG,CAACK,UAAUK,UAAU,EAA8BC,GAAG,CAAC,SAACV;eAAMA,EAAEZ,IAAI;;IACvK,IAAMuB,QAAQR,qBAAAA,sBAAAA,WAAY,AAACT,GAAGI,OAAO,CAAC,kCAAkCC,GAAG,GAA+BW,GAAG,CAAC,SAACV;eAAMA,EAAEZ,IAAI;;IAC3H,OAAO,IAAID,IAAIwB,MAAMC,MAAM,CAAC,SAACC;eAAMjC,QAAQiC,GAAGxB,SAASC;;AACzD;AAEO,SAASR,cAAcY,EAAgB,EAAEiB,KAAkB,EAAEG,KAAyB;IAC3F,IAAI,CAACA,OAAO,OAAOH;IACnB,IAAII;IACJ,IAAI;QACFA,YAAYrB,GAAGI,OAAO,CAAC,AAAC,2CAAgD,OAANgB,OAAM,MAAIf,GAAG;IACjF,EAAE,OAAOiB,KAAK;QACZ,MAAMC,IAAAA,wBAAU,EAACvB,IAAIsB;IACvB;IACA,IAAME,aAAa,IAAI/B,IAAI4B,UAAUL,GAAG,CAAC,SAACV;eAAMA,EAAEZ,IAAI;;IACtD,OAAO,IAAID,IAAI,AAAC,qBAAGwB,OAAOC,MAAM,CAAC,SAACC;eAAMK,WAAWjB,GAAG,CAACY;;AACzD;AAIO,SAAS5B,YAAYS,EAAgB,EAAEC,GAAmB,EAAEO,SAA0B;IAC3F,IAAME,YAAYC,IAAAA,sBAAa,EAACV,KAAKO;IACrC,OAAOpB,cAAcY,IAAIX,SAASW,IAAIC,KAAKO,YAAYE,UAAUU,KAAK;AACxE;AAIO,SAASjC,iBAAiBa,EAAgB,EAAEyB,KAAa,EAAER,KAAkB;IAClFjB,GAAG0B,IAAI,CAAC,AAAC,wBAA6B,OAAND;IAChCzB,GAAG0B,IAAI,CAAC,AAAC,qBAA0B,OAAND,OAAM;IACnCzB,GAAGI,OAAO,CAAC,AAAC,eAAoB,OAANqB,OAAM,8CAA4CE,GAAG,CAACC,KAAKC,SAAS,CAAE,qBAAGZ;AACrG;AAEO,SAASzB,cAAcQ,EAAgB,EAAEiB,KAAkB;IAChE9B,iBAAiBa,IAAI,cAAciB;AACrC"}

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 = "13";
+export declare const SCHEMA_VERSION = "14";
 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 = "13";
+export declare const SCHEMA_VERSION = "14";
 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 = '13';
+var SCHEMA_VERSION = '14';
 // 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 @@
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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 = '${tokenize}')`);\n  // Coverage, not ownership: a path can appear under several presets. path leads the PK so the\n  // per-doc delete is an index hit -- keyed the other way, cold builds went quadratic.\n  db.exec(`CREATE TABLE IF NOT EXISTS preset_files (\"path\" TEXT, preset TEXT, PRIMARY KEY (\"path\", preset))`);\n  db.exec('CREATE INDEX IF NOT EXISTS preset_files_preset ON preset_files(preset)');\n  for (const feature of activeFeatures(cfg)) feature.schema(db);\n  if (getMeta(db, 'schema_version') === null) setMeta(db, 'schema_version', SCHEMA_VERSION);\n  if (getMeta(db, 'features') === null) setMeta(db, 'features', featureSignature(cfg));\n}\n\nexport function docCount(db: DatabaseSync): number {\n  const row = db.prepare('SELECT COUNT(*) AS n FROM frontmatter').get() as { n: number };\n  return row.n;\n}\n\nexport function open(cfg: ResolvedConfig): OpenResult {\n  const stateDir = join(cfg.baseDir, STATE_DIR);\n  mkdirSync(stateDir, { recursive: true });\n  const dbPath = join(stateDir, DB_FILENAME);\n\n  const db = new DatabaseSync(dbPath);\n  db.exec('PRAGMA journal_mode = WAL');\n  // Covers a concurrent watcher's bulk reconcile (~5s for 500 files at 26k notes). 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It means no table\n// of which version added which tokenizer has to be maintained.\nfunction resolveTokenize(db: DatabaseSync, cfg: Config): string {\n  const configured = contentTokenize(cfg);\n  if (configured === undefined) return DEFAULT_TOKENIZE;\n  const literal = configured.replace(/'/g, \"''\");\n  try {\n    db.exec('DROP TABLE IF EXISTS temp.sense_tokenize_probe');\n    db.exec(`CREATE VIRTUAL TABLE temp.sense_tokenize_probe USING fts5(x, tokenize = '${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') ?? 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package/dist/cjs/features/links.js

@@ -66,10 +66,12 @@ function extract(_raw, body) {
     };
     var _iteratorNormalCompletion = true, _didIteratorError = false, _iteratorError = undefined;
     try {
-        for(var _iterator = body.matchAll(/\[\[([^\]|#]+)(?:#[^\]|]*)?(?:\|[^\]]*)?\]\]/g)[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true){
+        // 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 ].
+        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].trim();
+            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] === '!');
         }
     } catch (err) {
@@ -297,7 +299,13 @@ function resolveIncremental(db, delta) {
     return resolveRows(db, _to_consumable_array(candidates.values()), pathSet, byBase);
 }
 function linkEdges(db) {
-    return db.prepare('SELECT DISTINCT src, dst FROM links WHERE dst IS NOT NULL').all().map(function(r) {
+    // 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.
+    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)";
+    return db.prepare(sql).all().map(function(r) {
         return [
             r.src,
             r.dst

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  for (const m of body.matchAll(/\\[\\[([^\\]|#]+)(?:#[^\\]|]*)?(?:\\|[^\\]]*)?\\]\\]/g)) {\n    const target = m[1].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. DISTINCT: a target both linked\n// and embedded is two rows sharing one edge, which must not double its weight.\nexport function linkEdges(db: DatabaseSync): [string, string][] {\n  return (db.prepare('SELECT DISTINCT src, dst FROM links WHERE dst IS NOT NULL').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 (${placeholders})`).run(path, ...keys);\n    }\n    if (Number(stale.changes) > 0) recordRemoved(delta, path);\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same\n    // value and reports no change; only genuinely new rows start at NULL.\n    const insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) 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The only exclusion is an\n  // embed whose exact (src, target) also exists as a link: that second row is new with the\n  // embed grain and would double an edge that used to be one row. The NOT EXISTS probes the\n  // primary key and fires only for embed rows; both branches still scan the table.\n  const sql = `SELECT src, dst FROM links WHERE dst IS NOT NULL AND embed = 0\n    UNION ALL\n    SELECT src, dst FROM links l WHERE dst IS NOT NULL AND embed = 1\n      AND NOT EXISTS (SELECT 1 FROM links l0 WHERE l0.src = l.src AND l0.target = l.target AND l0.embed = 0)`;\n  return (db.prepare(sql).all() as Array<{ src: string; dst: string }>).map((r) => [r.src, r.dst]);\n}\n\n// remove() has already deleted the rows by the time afterReconcile runs, so it records here\n// whether they carried edges. 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'1' : '0'}`);\n      stale = db.prepare(`DELETE FROM links WHERE src = ? AND (target || char(0) || embed) NOT IN (${placeholders})`).run(path, ...keys);\n    }\n    if (Number(stale.changes) > 0) recordRemoved(delta, path);\n    // Upsert preserves dst on surviving rows, so an unchanged link resolves to the same\n    // value and reports no change; only genuinely new rows start at NULL.\n    const insert = db.prepare('INSERT INTO links (src, target, target_base, dst, embed) VALUES (?, ?, ?, NULL, ?) ON CONFLICT(src, target, embed) DO UPDATE SET target_base = excluded.target_base');\n    for (const { target, embed } of targets) insert.run(path, target, baseKey(cleanTarget(target)), embed ? 1 : 0);\n  },\n  afterReconcile(db, delta) {\n    // Any deleted rows that carried edges mean the edge set shrank -- whether the file\n    // vanished or was reparsed down to fewer/no links. dstChanged alone misses the\n    // reparsed-to-zero-links case (no surviving rows to re-resolve).\n    const removeHadLinks = (removedWithLinks.get(delta)?.size ?? 0) > 0;\n\n    const churn = delta.reparsed.length + delta.vanished.length;\n    // Past this share of the tree, a full pass is the only one guaranteed to match\n    // resolveTarget's ambiguity rules. A cold build clears the threshold on its own.\n    const large = delta.files.length === 0 || churn > 0.2 * delta.files.length;\n\n    const dstChanged = large ? resolveAll(db, delta.files) : resolveIncremental(db, delta);\n    delta.linksChanged = dstChanged || removeHadLinks;\n  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package/dist/cjs/features/tags.js

@@ -38,6 +38,10 @@ function _unsupported_iterable_to_array(o, minLen) {
 // (book/scifi); `tag = 'book' OR tag LIKE 'book/%'` is how a caller matches the parent too.
 var FENCE_RE = /^(```|~~~)/;
 var INLINE_CODE_RE = /`[^`]*`/g;
+// Obsidian treats [[#Heading]] as a same-note link, not a tag.
+var WIKILINK_RE = /\[\[.*?\]\]/g; // to the first ]], so a heading holding a lone ] still masks
+// Obsidian doesn't read tags inside HTML markup.
+var HTML_TAG_RE = /<\/?[a-zA-Z][^>]*>/g; // tag-shaped only: a comparison's `< 5` must not open a span
 // Anchors on start-of-line or a preceding whitespace/(/[ so `a#b` and URL fragments don't count.
 var INLINE_TAG_RE = 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"gu");
 // Strips a leading # (frontmatter entries may carry one) and a trailing /; rejects an
@@ -79,7 +83,7 @@ function frontmatterTags(data) {
     }
     return found;
 }
-// #tag tokens outside fenced code blocks and inline code spans.
+// #tag tokens outside fenced code blocks, inline code spans, wikilinks, and HTML tags.
 function inlineTags(body) {
     var found = [];
     var inFence = false;
@@ -92,7 +96,14 @@ function inlineTags(body) {
                 continue;
             }
             if (inFence) continue;
-            var cleaned = line.replace(INLINE_CODE_RE, function(m) {
+            if (!line.includes('#')) continue; // most lines; skip the regex work
+            var cleaned = line.includes('`') ? line.replace(INLINE_CODE_RE, function(m) {
+                return ' '.repeat(m.length);
+            }) : line;
+            if (cleaned.includes('[[')) cleaned = cleaned.replace(WIKILINK_RE, function(m) {
+                return ' '.repeat(m.length);
+            });
+            if (cleaned.includes('<')) cleaned = cleaned.replace(HTML_TAG_RE, function(m) {
                 return ' '.repeat(m.length);
             });
             var _iteratorNormalCompletion1 = true, _didIteratorError1 = false, _iteratorError1 = undefined;