sensemaking 0.7.2 → 0.8.0

package/dist/esm/cli/status.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/cli/status.ts"],"sourcesContent":["import { embedConfig, featureStates } from '../config.ts';\nimport { docCount, getMeta, open } from '../db.ts';\nimport { printWarnings } from './shared.ts';\nimport type { Command } from './types.ts';\n\n// Vectors are computed on the first semantic query, not at reconcile, so a tree can be\n// embed-enabled with nothing embedded yet -- reported here because a fast `rebuild` on an\n// embed tree otherwise reads as \"the feature isn't on\".\nfunction vectorState(db: ReturnType<typeof open>['db']): { embedded: number; pending: number } | null {\n  try {\n    const row = db.prepare('SELECT COUNT(vector) AS embedded, COUNT(*) - COUNT(vector) AS pending FROM embeddings').get() as { embedded: number; pending: number };\n    return row;\n  } catch {\n    return null;\n  }\n}\n\nconst status: Command = (ctx) => {\n  const cfg = ctx.resolveConfig();\n  const { db, dbPath, warnings } = open(cfg);\n  printWarnings(warnings);\n\n  const features = featureStates(cfg);\n  const e = embedConfig(cfg);\n  const vectors = e ? vectorState(db) : null;\n  const heartbeat = getMeta(db, 'watch_heartbeat');\n  // Derived at open() (F): 3x the largest reconcile this cache has ever held its write\n  // transaction for, floored at 30s -- read back from the connection rather than\n  // recomputed here, so this always reports what open() actually set.\n  const busyTimeoutMs = (db.prepare('PRAGMA busy_timeout').get() as { timeout: number }).timeout;\n  const result = {\n    db: dbPath,\n    docs: docCount(db),\n    features: features.on,\n    featuresOff: features.off,\n    embed: e ? { type: e.type, model: e.model, ...(vectors ?? {}) } : null,\n    findDefaultWhere: cfg.defaults?.find?.where ?? null,\n    watcherHeartbeatSecondsAgo: heartbeat ? 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package/dist/esm/cli/types.js.map

@@ -0,0 +1 @@
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package/dist/esm/cli/watch.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/cli/watch.ts"],"sourcesContent":["import type { WatchEvent } from '../watch.ts';\nimport { runWatch } from '../watch.ts';\nimport { printWarnings } from './shared.ts';\nimport type { Command } from './types.ts';\n\nconst watch: Command = async (ctx) => {\n  await runWatch(ctx.resolveConfig(), {\n    force: ctx.values.force,\n    onEvent: (event: WatchEvent) => {\n      if (event.type === 'started') {\n        console.log(`${ctx.name} watch: watching ${event.baseDir}`);\n        console.log(`${ctx.name} watch: db ${event.dbPath}`);\n      } else if (event.type === 'reconciled') {\n        printWarnings(event.warnings);\n        if (event.parsed > 0) console.log(`${ctx.name} watch: reconciled, ${event.parsed} file(s) reparsed (${event.total} total)`);\n      } else {\n        console.error(`${ctx.name} watch: reconcile error: ${event.message}`);\n      }\n    },\n  });\n};\nexport default watch;\n"],"names":["runWatch","printWarnings","watch","ctx","resolveConfig","force","values","onEvent","event","type","console","log","name","baseDir","dbPath","warnings","parsed","total","error","message"],"mappings":"AACA,SAASA,QAAQ,QAAQ,cAAc;AACvC,SAASC,aAAa,QAAQ,cAAc;AAG5C,MAAMC,QAAiB,OAAOC;IAC5B,MAAMH,SAASG,IAAIC,aAAa,IAAI;QAClCC,OAAOF,IAAIG,MAAM,CAACD,KAAK;QACvBE,SAAS,CAACC;YACR,IAAIA,MAAMC,IAAI,KAAK,WAAW;gBAC5BC,QAAQC,GAAG,CAAC,GAAGR,IAAIS,IAAI,CAAC,iBAAiB,EAAEJ,MAAMK,OAAO,EAAE;gBAC1DH,QAAQC,GAAG,CAAC,GAAGR,IAAIS,IAAI,CAAC,WAAW,EAAEJ,MAAMM,MAAM,EAAE;YACrD,OAAO,IAAIN,MAAMC,IAAI,KAAK,cAAc;gBACtCR,cAAcO,MAAMO,QAAQ;gBAC5B,IAAIP,MAAMQ,MAAM,GAAG,GAAGN,QAAQC,GAAG,CAAC,GAAGR,IAAIS,IAAI,CAAC,oBAAoB,EAAEJ,MAAMQ,MAAM,CAAC,mBAAmB,EAAER,MAAMS,KAAK,CAAC,OAAO,CAAC;YAC5H,OAAO;gBACLP,QAAQQ,KAAK,CAAC,GAAGf,IAAIS,IAAI,CAAC,yBAAyB,EAAEJ,MAAMW,OAAO,EAAE;YACtE;QACF;IACF;AACF;AACA,eAAejB,MAAM"}

package/dist/esm/cli.js

@@ -1,8 +1,8 @@
 import { createRequire } from 'node:module';
 import { parseArgs } from 'node:util';
-import { COMMANDS } from './commands/index.js';
+import { COMMANDS } from './cli/index.js';
 import { loadConfig, SUPPORTED_CONFIG_VERSION } from './config.js';
-// Parsing and dispatch only. Commands live in src/commands/, one file each, lazy-loaded --
+// Parsing and dispatch only. Commands live in src/cli/, one file each, lazy-loaded --
 // nothing tree- or dependency-heavy may be imported at the top of this file.
 // Works from dist/cjs and dist/esm alike: walk up past the dist type-marker package.json.
 function packageVersion() {
@@ -44,8 +44,7 @@ export default async function cli(argv, name) {
                     type: 'string'
                 },
                 semantic: {
-                    type: 'boolean',
-                    default: false
+                    type: 'boolean'
                 },
                 list: {
                     type: 'boolean',
@@ -103,7 +102,10 @@ export default async function cli(argv, name) {
     };
     try {
         if (values.list) {
-            for (const queryName of Object.keys(ctx.resolveConfig().queries).sort())console.log(queryName);
+            const queries = ctx.resolveConfig().queries;
+            for (const queryName of Object.keys(queries).sort()){
+                console.log(typeof queries[queryName] === 'string' ? queryName : `${queryName}  (find)`);
+            }
             return;
         }
         const [first, ...params] = positionals;
@@ -113,7 +115,7 @@ export default async function cli(argv, name) {
         }
         const load = COMMANDS[first];
         if (load) await (await load()).default(ctx);
-        else (await import('./commands/named.js')).default(ctx, first, params);
+        else await (await import('./cli/named.js')).default(ctx, first, params);
     } catch (err) {
         console.error(err.message);
         process.exit(1);

package/dist/esm/cli.js.map

@@ -1 +1 @@
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Commands live in src/cli/, one file each, lazy-loaded --\n// nothing tree- or dependency-heavy may be imported at the top of this file.\n\n// Works from dist/cjs and dist/esm alike: walk up past the dist type-marker package.json.\nfunction packageVersion(): string {\n  const load = createRequire(import.meta.url);\n  for (const rel of ['../package.json', '../../package.json', '../../../package.json']) {\n    try {\n      const pkg = load(rel) as { name?: string; version?: string };\n      if (pkg.name === 'sensemaking' && pkg.version) return pkg.version;\n    } catch {}\n  }\n  return 'unknown';\n}\n\nfunction usage(name: string): string {\n  return (\n    `usage: ${name} <name> [params...] [--format table|json] [--config path]\\n` +\n    `       ${name} query \"<sql>\" [params...]\\n` +\n    `       ${name} find \"<terms>\" [--where \"<sql>\"] [--k n] [--semantic]\\n` +\n    `       ${name} map\\n` +\n    `       ${name} peek <path>\\n` +\n    `       ${name} --list\\n` +\n    `       ${name} init\\n` +\n    `       ${name} watch [--force]\\n` +\n    `       ${name} status\\n` +\n    `       ${name} check\\n` +\n    `       ${name} rebuild\\n` +\n    `       ${name} --version`\n  );\n}\n\n// Thrown errors -> exit 1 with the message verbatim; usage errors exit 2 directly.\nexport default async function cli(argv: string[], name: string): Promise<void> {\n  let values: Record<string, string | boolean | undefined>;\n  let positionals: string[];\n  try {\n    ({ values, positionals } = parseArgs({\n      args: argv,\n      options: {\n        format: { type: 'string', default: 'table' },\n        config: { type: 'string' },\n        where: { type: 'string' },\n        k: { type: 'string' },\n        semantic: { type: 'boolean' },\n        list: { type: 'boolean', default: false },\n        force: { type: 'boolean', default: false },\n        version: { type: 'boolean', default: false, short: 'v' },\n        help: { type: 'boolean', default: false, short: 'h' },\n      },\n      allowPositionals: true,\n    }));\n  } catch (err) {\n    console.error((err as Error).message);\n    console.error(usage(name));\n    process.exit(2);\n  }\n\n  if (values.version) {\n    console.log(`v${packageVersion()}`);\n    return;\n  }\n  if (values.help) {\n    console.log(usage(name));\n    return;\n  }\n\n  const ctx: Ctx = {\n    name,\n    rest: positionals.slice(1),\n    format: values.format === 'json' ? 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package/dist/{cjs/verbs.d.ts → esm/commands.d.ts}

@@ -1,12 +1,12 @@
 import type { DatabaseSync } from 'node:sqlite';
-import type { Config, FeatureName } from './config.js';
+import type { FeatureName, ResolvedConfig } from './config.js';
 import type { Row } from './output.js';
 export interface FindOptions {
     k?: number;
     where?: string;
     semantic?: boolean;
 }
-export declare function find(db: DatabaseSync, cfg: Config, terms: string, opts?: FindOptions): Promise<Row[]>;
+export declare function find(db: DatabaseSync, cfg: ResolvedConfig, terms: string, opts?: FindOptions): Promise<Row[]>;
 export interface TreeMap {
     docs: {
         count: number;
@@ -21,7 +21,7 @@ export interface TreeMap {
     hubs: Row[];
     recent: Row[];
 }
-export declare function mapTree(db: DatabaseSync, cfg: Config): TreeMap;
+export declare function mapTree(db: DatabaseSync, cfg: ResolvedConfig): TreeMap;
 export interface Peek {
     path: string;
     tokens: number;
@@ -30,9 +30,10 @@ export interface Peek {
     outbound: string[];
     backlinks: string[];
     unresolved: string[];
+    sectionsTotal: number;
     outboundTotal: number;
     backlinksTotal: number;
     unresolvedTotal: number;
     off: FeatureName[];
 }
-export declare function peek(db: DatabaseSync, cfg: Config, pathArg: string): Peek;
+export declare function peek(db: DatabaseSync, cfg: ResolvedConfig, pathArg: string): Peek;

package/dist/esm/{verbs.js → commands.js}

@@ -1,3 +1,5 @@
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 import posix from 'node:path/posix';
 import { featureEnabled, featureStates } from './config.js';
 import { SenseError } from './errors.js';
@@ -5,10 +7,108 @@ import { semanticCandidates } from './features/embed.js';
 import { linkEdges } from './features/index.js';
 import { personalizedRank } from './graph.js';
 import { searchError } from './search-error.js';
-// The three layer verbs: mapTree (orient), find (locate), peek (structure).
+// The three layer commands: mapTree (orient), find (locate), peek (structure).
 // Each returns data; cli.ts renders. All of them degrade when a feature is off.
 const WEIGHTED_BM25 = 'bm25(content, 10.0, 5.0, 1.0)';
 const RRF_K = 60;
+// FTS5 snippet() re-tokenizes the whole doc per candidate row, superlinearly: measured
+// 2ms at 4KB docs but 189ms at 64KB for one query's pool, and ~10s for a single 1MB doc
+// (plans/performance-findings.md finding A). 16KB keeps the whole pool's snippet cost in
+// the low-ms range; bigger docs get the JS-computed excerpt, linear and only for the rows
+// actually returned.
+const SNIPPET_BOUND = 16384;
+const EXCERPT_WINDOW = 160;
+// Bare terms from an FTS5 query string: strips operators/quoting so the oversized-doc excerpt
+// scan matches the same words the query matched on, not FTS5 syntax.
+function extractBareTerms(query) {
+    const cleaned = query.replace(/"/g, ' ').replace(/[()*]/g, ' ').replace(/\b(AND|OR|NOT|NEAR)\b(\/\d+)?/gi, ' ');
+    return cleaned.split(/\s+/).map((tok)=>tok.replace(/^[A-Za-z_]\w*:/, '')) // column filter, e.g. title:term
+    .map((tok)=>tok.toLowerCase().trim()).filter((tok)=>tok.length > 0);
+}
+function findOccurrences(haystackLower, terms) {
+    const occ = [];
+    for (const term of terms){
+        let idx = 0;
+        for(;;){
+            const found = haystackLower.indexOf(term, idx);
+            if (found === -1) break;
+            occ.push({
+                start: found,
+                end: found + term.length,
+                term
+            });
+            idx = found + term.length;
+        }
+    }
+    // Longest span first at equal start, so "tests" beats its substring "test" and the
+    // whole word gets highlighted; the emit loop then absorbs the shorter overlap.
+    return occ.sort((a, b)=>a.start - b.start || b.end - a.end);
+}
+// Slides a window over the sorted occurrences, same semantics as FTS5's own best-window
+// pick: most distinct terms, ties broken by most total hits.
+function bestWindowStart(occ, windowSize) {
+    let best = occ[0].start;
+    let bestDistinct = 0;
+    let bestCount = 0;
+    for(let i = 0; i < occ.length; i++){
+        const winEnd = occ[i].start + windowSize;
+        const seen = new Set();
+        let count = 0;
+        for(let j = i; j < occ.length && occ[j].start < winEnd; j++){
+            seen.add(occ[j].term);
+            count++;
+        }
+        if (seen.size > bestDistinct || seen.size === bestDistinct && count > bestCount) {
+            best = occ[i].start;
+            bestDistinct = seen.size;
+            bestCount = count;
+        }
+    }
+    return best;
+}
+// snippet()-shaped excerpt: matched terms wrapped in «», … at cut edges. Linear in doc
+// length, only run for rows actually returned (<= k), unlike snippet()'s per-row cost.
+function computeExcerpt(text, terms) {
+    const occ = findOccurrences(text.toLowerCase(), terms);
+    if (occ.length === 0) {
+        // This is a raw substring scan, not porter-stemmed: a doc matched only through a
+        // stemmed variant (query "negotiate" vs doc "negotiating") finds no occurrence here.
+        // Fall back to the doc's start, unmarked, rather than claim a match that isn't there.
+        const end = Math.min(text.length, EXCERPT_WINDOW);
+        return {
+            excerpt: `${text.slice(0, end).replace(/\s+/g, ' ').trim()}${end < text.length ? '…' : ''}`,
+            offset: 0
+        };
+    }
+    const start = bestWindowStart(occ, EXCERPT_WINDOW);
+    const end = Math.min(text.length, start + EXCERPT_WINDOW);
+    let out = '';
+    let cursor = start;
+    for (const o of occ){
+        if (o.start < start || o.end > end) continue;
+        // Occurrences of duplicate or substring-overlapping terms ("test tests") can overlap;
+        // emitting each would duplicate document text. Keep the first, absorb the rest.
+        if (o.start < cursor) continue;
+        out += `${text.slice(cursor, o.start)}«${text.slice(o.start, o.end)}»`;
+        cursor = o.end;
+    }
+    out += text.slice(cursor, end);
+    const prefix = start > 0 ? '…' : '';
+    const suffix = end < text.length ? '…' : '';
+    return {
+        excerpt: `${prefix}${out.replace(/\s+/g, ' ')}${suffix}`,
+        offset: start
+    };
+}
+function lineNumberAt(text, offset) {
+    let line = 1;
+    for(let i = 0; i < offset; i++)if (text.charCodeAt(i) === 10) line++;
+    return line;
+}
+function lineRangeFor(db, path, line) {
+    const row = db.prepare('SELECT start_line, end_line FROM sections WHERE "path" = ? AND start_line <= ? AND end_line >= ? ORDER BY start_line DESC LIMIT 1').get(path, line, line);
+    return row ? `L${row.start_line}-${row.end_line}` : null;
+}
 // Layer 1: BM25 + link-graph expansion, fused by reciprocal rank. `via` says which
 // signal produced each row so the agent knows what evidence it is trusting.
 // Semantic expansion is per-query opt-in: without opts.semantic the result is
@@ -27,7 +127,9 @@ export async function find(db, cfg, terms, opts = {}) {
     const scope = (_opts_where = opts.where) !== null && _opts_where !== void 0 ? _opts_where : (_cfg_defaults = cfg.defaults) === null || _cfg_defaults === void 0 ? void 0 : (_cfg_defaults_find = _cfg_defaults.find) === null || _cfg_defaults_find === void 0 ? void 0 : _cfg_defaults_find.where;
     const whereJoin = scope ? `JOIN frontmatter f ON f."path" = content.path` : '';
     const whereCond = scope ? `AND (${scope})` : '';
-    const matchSql = `SELECT content.path AS path, snippet(content, -1, '«', '»', '…', 10) AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;
+    // Docs past SNIPPET_BOUND skip snippet() entirely -- SQLite
+    // short-circuits the untaken CASE branch, so it's never invoked on them.
+    const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, -1, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;
     let matchRows;
     try {
         matchRows = db.prepare(matchSql).all(terms);
@@ -38,6 +140,9 @@ export async function find(db, cfg, terms, opts = {}) {
             r.path,
             r.hit
         ]));
+    // hit === null here means the bound suppressed snippet(), not "no match" -- distinguish
+    // from via='link' rows (never in matchRows, so absent from this set) below.
+    const oversized = new Set(matchRows.filter((r)=>r.hit === null).map((r)=>r.path));
     const candidates = new Map();
     matchRows.forEach((r, i)=>{
         candidates.set(r.path, {
@@ -99,10 +204,28 @@ export async function find(db, cfg, terms, opts = {}) {
     const insert = db.prepare('INSERT INTO _find ("path", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');
     for (const [path, c] of candidates)insert.run(path, c.score, c.via, (_hits_get = hits.get(path)) !== null && _hits_get !== void 0 ? _hits_get : null, (_chunkLines_get = chunkLines.get(path)) !== null && _chunkLines_get !== void 0 ? _chunkLines_get : null, (_chunkSimilarity_get = chunkSimilarity.get(path)) !== null && _chunkSimilarity_get !== void 0 ? _chunkSimilarity_get : null);
     const where = scope ? `WHERE ${scope}` : '';
-    const linesCol = opts.semantic ? ', _find.lines, _find.similarity' : '';
-    return db.prepare(`SELECT f."path" AS path, content.title, content.summary, _find.hit, _find.via, round(_find.score, 4) AS score${linesCol}
+    // lines is always present now: semantic rows carry their chunk's range, oversized-doc
+    // lexical rows gain one below, everything else stays null. similarity stays semantic-only.
+    const similarityCol = opts.semantic ? ', _find.similarity' : '';
+    const rows = db.prepare(`SELECT f."path" AS path, content.title, content.summary, _find.hit, _find.via, round(_find.score, 4) AS score, _find.lines${similarityCol}
        FROM _find JOIN frontmatter f ON f."path" = _find."path" JOIN content ON content.path = _find."path"
        ${where} ORDER BY _find.score DESC LIMIT ?`).all(k);
+    if (oversized.size > 0) {
+        const bareTerms = extractBareTerms(terms);
+        for (const row of rows){
+            if (row.hit !== null || !oversized.has(row.path)) continue;
+            let text;
+            try {
+                text = readFileSync(join(cfg.baseDir, row.path), 'utf8');
+            } catch  {
+                continue; // vanished since the match; leave hit/lines null rather than throw
+            }
+            const { excerpt, offset } = computeExcerpt(text, bareTerms);
+            row.hit = excerpt;
+            if (row.lines == null) row.lines = featureEnabled(cfg, 'sections') ? lineRangeFor(db, row.path, lineNumberAt(text, offset)) : null;
+        }
+    }
+    return rows;
 }
 const INTERNAL_COLUMNS = new Set([
     'path',
@@ -110,22 +233,41 @@ const INTERNAL_COLUMNS = new Set([
     '_size',
     '_rank'
 ]);
+// A result row is capped at SQLITE_MAX_COLUMN (2000, default); two aggregate expressions
+// per field keeps a chunk's row safely under that regardless of how many fields the tree has.
+const MAP_COLUMN_CHUNK = 300;
+function chunk(items, size) {
+    const out = [];
+    for(let i = 0; i < items.length; i += size)out.push(items.slice(i, i + size));
+    return out;
+}
 // Layer 0: what is this tree. Fixed-size output regardless of tree size.
 export function mapTree(db, cfg) {
     const docs = db.prepare('SELECT COUNT(*) AS count, COALESCE(SUM("_size"), 0) AS bytes FROM frontmatter').get();
     const columns = db.prepare('PRAGMA table_info(frontmatter)').all().map((r)=>r.name).filter((name)=>!INTERNAL_COLUMNS.has(name));
-    const allFields = columns.map((name)=>{
-        const quoted = `"${name.split('"').join('""')}"`;
-        // Observed storage class, not a declared one: these columns are added dynamically and
-        // SQLite types per value, so a field can be text in most notes and numeric in a few.
-        // Listing every distinct type makes both the type and any drift visible.
-        const { n, types } = db.prepare(`SELECT COUNT(${quoted}) AS n, GROUP_CONCAT(DISTINCT typeof(${quoted})) AS types FROM frontmatter WHERE ${quoted} IS NOT NULL`).get();
-        return {
-            field: name,
-            coverage: n,
-            type: types !== null && types !== void 0 ? types : ''
-        };
-    }).sort((a, b)=>b.coverage - a.coverage);
+    // Observed storage class, not a declared one: these columns are added dynamically and
+    // SQLite types per value, so a field can be text in most notes and numeric in a few.
+    // Listing every distinct type makes both the type and any drift visible.
+    // One aggregate scan per chunk of columns rather than one scan per column: COUNT already
+    // ignores NULL, and FILTER keeps typeof() looking only at the non-null rows COUNT counted,
+    // matching the old per-column `WHERE ... IS NOT NULL` exactly.
+    const allFields = [];
+    for (const group of chunk(columns, MAP_COLUMN_CHUNK)){
+        const exprs = group.map((name, i)=>{
+            const quoted = `"${name.split('"').join('""')}"`;
+            return `COUNT(${quoted}) AS n${i}, GROUP_CONCAT(DISTINCT typeof(${quoted})) FILTER (WHERE ${quoted} IS NOT NULL) AS t${i}`;
+        });
+        const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter`).get();
+        group.forEach((name, i)=>{
+            var _result_;
+            return allFields.push({
+                field: name,
+                coverage: result[`n${i}`],
+                type: (_result_ = result[`t${i}`]) !== null && _result_ !== void 0 ? _result_ : ''
+            });
+        });
+    }
+    allFields.sort((a, b)=>b.coverage - a.coverage);
     const fields = allFields.slice(0, 20);
     const hubs = featureEnabled(cfg, 'rank') ? db.prepare(`SELECT f."path" AS path, round(f."_rank" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f."path" WHERE f."_rank" IS NOT NULL ORDER BY f."_rank" DESC LIMIT 8`).all() : [];
     const recent = db.prepare(`SELECT "path", datetime("_mtime" / 1000, 'unixepoch') AS modified FROM frontmatter ORDER BY "_mtime" DESC LIMIT 5`).all();
@@ -138,7 +280,7 @@ export function mapTree(db, cfg) {
         recent
     };
 }
-const PEEK_LINK_LIMIT = 20;
+const PEEK_LIST_LIMIT = 20;
 // Layer 2: everything about one note except its prose -- frontmatter, outline with line
 // ranges + token estimates (so the follow-up Read is a range, not the file), links both ways.
 export function peek(db, cfg, pathArg) {
@@ -157,7 +299,8 @@ export function peek(db, cfg, pathArg) {
     for (const [key, value] of Object.entries(row)){
         if (!INTERNAL_COLUMNS.has(key) && value !== null) frontmatter[key] = value;
     }
-    const sections = featureEnabled(cfg, 'sections') ? db.prepare('SELECT level, heading, start_line, end_line, tokens FROM sections WHERE "path" = ? ORDER BY idx').all(path) : [];
+    const sectionsTotal = featureEnabled(cfg, 'sections') ? db.prepare('SELECT COUNT(*) AS n FROM sections WHERE "path" = ?').get(path).n : 0;
+    const sections = featureEnabled(cfg, 'sections') ? db.prepare('SELECT level, heading, start_line, end_line, tokens FROM sections WHERE "path" = ? ORDER BY idx LIMIT ?').all(path, PEEK_LIST_LIMIT) : [];
     let outbound = [];
     let backlinks = [];
     let unresolved = [];
@@ -169,16 +312,17 @@ export function peek(db, cfg, pathArg) {
         ];
         unresolved = out.filter((l)=>l.dst === null).map((l)=>l.target);
         backlinksTotal = db.prepare('SELECT COUNT(DISTINCT src) AS n FROM links WHERE dst = ?').get(path).n;
-        backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? ORDER BY src LIMIT ?').all(path, PEEK_LINK_LIMIT).map((r)=>r.src);
+        backlinks = db.prepare('SELECT DISTINCT src FROM links WHERE dst = ? ORDER BY src LIMIT ?').all(path, PEEK_LIST_LIMIT).map((r)=>r.src);
     }
     return {
         path,
         tokens: Math.ceil(((_row__size = row._size) !== null && _row__size !== void 0 ? _row__size : 0) / 4),
         frontmatter,
         sections,
-        outbound: outbound.slice(0, PEEK_LINK_LIMIT),
+        outbound: outbound.slice(0, PEEK_LIST_LIMIT),
         backlinks,
-        unresolved: unresolved.slice(0, PEEK_LINK_LIMIT),
+        unresolved: unresolved.slice(0, PEEK_LIST_LIMIT),
+        sectionsTotal,
         outboundTotal: outbound.length,
         backlinksTotal,
         unresolvedTotal: unresolved.length,

package/dist/esm/commands.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["/Users/kevin/Dev/OpenSource/ai/sensemaking/src/commands.ts"],"sourcesContent":["import { readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport posix from 'node:path/posix';\nimport type { DatabaseSync } from 'node:sqlite';\nimport type { FeatureName, ResolvedConfig } from './config.ts';\nimport { featureEnabled, featureStates } from './config.ts';\nimport { SenseError } from './errors.ts';\nimport { semanticCandidates } from './features/embed.ts';\nimport { linkEdges } from './features/index.ts';\nimport { personalizedRank } from './graph.ts';\nimport type { Row } from './output.ts';\nimport { searchError } from './search-error.ts';\n\n// The three layer commands: mapTree (orient), find (locate), peek (structure).\n// Each returns data; cli.ts renders. All of them degrade when a feature is off.\n\nconst WEIGHTED_BM25 = 'bm25(content, 10.0, 5.0, 1.0)';\nconst RRF_K = 60;\n\n// FTS5 snippet() re-tokenizes the whole doc per candidate row, superlinearly: measured\n// 2ms at 4KB docs but 189ms at 64KB for one query's pool, and ~10s for a single 1MB doc\n// (plans/performance-findings.md finding A). 16KB keeps the whole pool's snippet cost in\n// the low-ms range; bigger docs get the JS-computed excerpt, linear and only for the rows\n// actually returned.\nconst SNIPPET_BOUND = 16_384;\nconst EXCERPT_WINDOW = 160;\n\n// Bare terms from an FTS5 query string: strips operators/quoting so the oversized-doc excerpt\n// scan matches the same words the query matched on, not FTS5 syntax.\nfunction extractBareTerms(query: string): string[] {\n  const cleaned = query\n    .replace(/\"/g, ' ')\n    .replace(/[()*]/g, ' ')\n    .replace(/\\b(AND|OR|NOT|NEAR)\\b(\\/\\d+)?/gi, ' ');\n  return cleaned\n    .split(/\\s+/)\n    .map((tok) => tok.replace(/^[A-Za-z_]\\w*:/, '')) // column filter, e.g. title:term\n    .map((tok) => tok.toLowerCase().trim())\n    .filter((tok) => tok.length > 0);\n}\n\nfunction findOccurrences(haystackLower: string, terms: string[]): Array<{ start: number; end: number; term: string }> {\n  const occ: Array<{ start: number; end: number; term: string }> = [];\n  for (const term of terms) {\n    let idx = 0;\n    for (;;) {\n      const found = haystackLower.indexOf(term, idx);\n      if (found === -1) break;\n      occ.push({ start: found, end: found + term.length, term });\n      idx = found + term.length;\n    }\n  }\n  // Longest span first at equal start, so \"tests\" beats its substring \"test\" and the\n  // whole word gets highlighted; the emit loop then absorbs the shorter overlap.\n  return occ.sort((a, b) => a.start - b.start || b.end - a.end);\n}\n\n// Slides a window over the sorted occurrences, same semantics as FTS5's own best-window\n// pick: most distinct terms, ties broken by most total hits.\nfunction bestWindowStart(occ: Array<{ start: number; end: number; term: string }>, windowSize: number): number {\n  let best = occ[0].start;\n  let bestDistinct = 0;\n  let bestCount = 0;\n  for (let i = 0; i < occ.length; i++) {\n    const winEnd = occ[i].start + windowSize;\n    const seen = new Set<string>();\n    let count = 0;\n    for (let j = i; j < occ.length && occ[j].start < winEnd; j++) {\n      seen.add(occ[j].term);\n      count++;\n    }\n    if (seen.size > bestDistinct || (seen.size === bestDistinct && count > bestCount)) {\n      best = occ[i].start;\n      bestDistinct = seen.size;\n      bestCount = count;\n    }\n  }\n  return best;\n}\n\n// snippet()-shaped excerpt: matched terms wrapped in «», … at cut edges. Linear in doc\n// length, only run for rows actually returned (<= k), unlike snippet()'s per-row cost.\nfunction computeExcerpt(text: string, terms: string[]): { excerpt: string; offset: number } {\n  const occ = findOccurrences(text.toLowerCase(), terms);\n  if (occ.length === 0) {\n    // This is a raw substring scan, not porter-stemmed: a doc matched only through a\n    // stemmed variant (query \"negotiate\" vs doc \"negotiating\") finds no occurrence here.\n    // Fall back to the doc's start, unmarked, rather than claim a match that isn't there.\n    const end = Math.min(text.length, EXCERPT_WINDOW);\n    return { excerpt: `${text.slice(0, end).replace(/\\s+/g, ' ').trim()}${end < text.length ? '…' : ''}`, offset: 0 };\n  }\n  const start = bestWindowStart(occ, EXCERPT_WINDOW);\n  const end = Math.min(text.length, start + EXCERPT_WINDOW);\n  let out = '';\n  let cursor = start;\n  for (const o of occ) {\n    if (o.start < start || o.end > end) continue;\n    // Occurrences of duplicate or substring-overlapping terms (\"test tests\") can overlap;\n    // emitting each would duplicate document text. Keep the first, absorb the rest.\n    if (o.start < cursor) continue;\n    out += `${text.slice(cursor, o.start)}«${text.slice(o.start, o.end)}»`;\n    cursor = o.end;\n  }\n  out += text.slice(cursor, end);\n  const prefix = start > 0 ? '…' : '';\n  const suffix = end < text.length ? '…' : '';\n  return { excerpt: `${prefix}${out.replace(/\\s+/g, ' ')}${suffix}`, offset: start };\n}\n\nfunction lineNumberAt(text: string, offset: number): number {\n  let line = 1;\n  for (let i = 0; i < offset; i++) if (text.charCodeAt(i) === 10) line++;\n  return line;\n}\n\nfunction lineRangeFor(db: DatabaseSync, path: string, line: number): string | null {\n  const row = db.prepare('SELECT start_line, end_line FROM sections WHERE \"path\" = ? AND start_line <= ? AND end_line >= ? ORDER BY start_line DESC LIMIT 1').get(path, line, line) as { start_line: number; end_line: number } | undefined;\n  return row ? `L${row.start_line}-${row.end_line}` : null;\n}\n\nexport interface FindOptions {\n  k?: number;\n  where?: string; // SQL fragment against frontmatter alias `f`, e.g. \"f.status = 'active'\"\n  semantic?: boolean; // invoke vector expansion (requires features.embed); rows gain via 'vector' and a lines column\n}\n\n// Layer 1: BM25 + link-graph expansion, fused by reciprocal rank. `via` says which\n// signal produced each row so the agent knows what evidence it is trusting.\n// Semantic expansion is per-query opt-in: without opts.semantic the result is\n// byte-for-byte independent of the embed feature.\nexport async function find(db: DatabaseSync, cfg: ResolvedConfig, terms: string, opts: FindOptions = {}): Promise<Row[]> {\n  const k = opts.k ?? 10;\n  const fetch = Math.max(k * 3, 30);\n\n  // Terms pass verbatim to FTS5 MATCH: bare words AND-join, operators are the caller's.\n  // Invalid syntax propagates as an error, zero matches return zero -- no silent rewrites.\n  // --where applies inside the candidate query (a post-filter over the top-N would drop\n  // matches ranked past the pool) and again on the final select for link-derived rows.\n  // An explicit --where replaces the tree's declared default rather than ANDing with it,\n  // so a caller can always widen back to the whole tree.\n  const scope = opts.where ?? cfg.defaults?.find?.where;\n  const whereJoin = scope ? `JOIN frontmatter f ON f.\"path\" = content.path` : '';\n  const whereCond = scope ? `AND (${scope})` : '';\n  // Docs past SNIPPET_BOUND skip snippet() entirely -- SQLite\n  // short-circuits the untaken CASE branch, so it's never invoked on them.\n  const matchSql = `SELECT content.path AS path, CASE WHEN length(content.text) <= ${SNIPPET_BOUND} THEN snippet(content, -1, '«', '»', '…', 10) ELSE NULL END AS hit FROM content ${whereJoin} WHERE content MATCH ? ${whereCond} ORDER BY ${WEIGHTED_BM25} LIMIT ${fetch}`;\n  let matchRows: Array<{ path: string; hit: string | null }>;\n  try {\n    matchRows = db.prepare(matchSql).all(terms) as Array<{ path: string; hit: string | null }>;\n  } catch (err) {\n    throw searchError(err as Error, terms, scope);\n  }\n\n  const hits = new Map(matchRows.map((r) => [r.path, r.hit]));\n  // hit === null here means the bound suppressed snippet(), not \"no match\" -- distinguish\n  // from via='link' rows (never in matchRows, so absent from this set) below.\n  const oversized = new Set(matchRows.filter((r) => r.hit === null).map((r) => r.path));\n  const candidates = new Map<string, { score: number; via: string }>();\n  matchRows.forEach((r, i) => {\n    candidates.set(r.path, { score: 1 / (RRF_K + i), via: 'match' });\n  });\n\n  const edges = featureEnabled(cfg, 'links') && matchRows.length > 0 ? linkEdges(db) : [];\n  if (edges.length > 0) {\n    // `linked` gates the label only, not the score: PPR restart mass gives every seed a\n    // nonzero rank even without an incident edge, which is not link evidence — but dropping\n    // that mass from the score list reweights fusion toward connectivity and measurably\n    // wrecks ranking on link-dense corpora (FEVER hit@10 0.997 -> 0.907; fusion-tuning.md).\n    const linked = new Set(edges.flat());\n    const nodes = (db.prepare('SELECT \"path\" FROM frontmatter').all() as Array<{ path: string }>).map((r) => r.path);\n    const seeds = new Map(matchRows.map((r, i) => [r.path, 1 / (i + 1)]));\n    const ranked = [...personalizedRank(nodes, edges, seeds)]\n      .filter(([, score]) => score > 1e-9)\n      .sort((a, b) => b[1] - a[1])\n      .slice(0, fetch);\n    ranked.forEach(([path], i) => {\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        if (linked.has(path)) existing.via = 'match+link';\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'link' });\n      }\n    });\n  }\n\n  // Vector expansion, invoked only: a third RRF list at the swept flat-region constants\n  // (weight 1, pool = fetch). Each row carries its best chunk's line range.\n  const chunkLines = new Map<string, string>();\n  const chunkSimilarity = new Map<string, number>();\n  if (opts.semantic) {\n    const vec = await semanticCandidates(db, cfg, terms, fetch);\n    vec.forEach(({ path, lines, similarity }, i) => {\n      chunkLines.set(path, lines);\n      chunkSimilarity.set(path, similarity);\n      const existing = candidates.get(path);\n      if (existing) {\n        existing.score += 1 / (RRF_K + i);\n        existing.via = `${existing.via}+vector`;\n      } else {\n        candidates.set(path, { score: 1 / (RRF_K + i), via: 'vector' });\n      }\n    });\n  }\n\n  db.exec('DROP TABLE IF EXISTS _find');\n  db.exec('CREATE TEMP TABLE _find (\"path\" TEXT PRIMARY KEY, score REAL, via TEXT, hit TEXT, lines TEXT, similarity REAL)');\n  const insert = db.prepare('INSERT INTO _find (\"path\", score, via, hit, lines, similarity) VALUES (?, ?, ?, ?, ?, ?)');\n  for (const [path, c] of candidates) insert.run(path, c.score, c.via, hits.get(path) ?? null, chunkLines.get(path) ?? null, chunkSimilarity.get(path) ?? null);\n\n  const where = scope ? `WHERE ${scope}` : '';\n  // lines is always present now: semantic rows carry their chunk's range, oversized-doc\n  // lexical rows gain one below, everything else stays null. similarity stays semantic-only.\n  const similarityCol = opts.semantic ? ', _find.similarity' : '';\n  const rows = db\n    .prepare(\n      `SELECT f.\"path\" AS path, content.title, content.summary, _find.hit, _find.via, round(_find.score, 4) AS score, _find.lines${similarityCol}\n       FROM _find JOIN frontmatter f ON f.\"path\" = _find.\"path\" JOIN content ON content.path = _find.\"path\"\n       ${where} ORDER BY _find.score DESC LIMIT ?`\n    )\n    .all(k) as Row[];\n\n  if (oversized.size > 0) {\n    const bareTerms = extractBareTerms(terms);\n    for (const row of rows) {\n      if (row.hit !== null || !oversized.has(row.path as string)) continue;\n      let text: string;\n      try {\n        text = readFileSync(join(cfg.baseDir, row.path as string), 'utf8');\n      } catch {\n        continue; // vanished since the match; leave hit/lines null rather than throw\n      }\n      const { excerpt, offset } = computeExcerpt(text, bareTerms);\n      row.hit = excerpt;\n      if (row.lines == null) row.lines = featureEnabled(cfg, 'sections') ? lineRangeFor(db, row.path as string, lineNumberAt(text, offset)) : null;\n    }\n  }\n\n  return rows;\n}\n\nexport interface TreeMap {\n  docs: { count: number; bytes: number };\n  fields: Row[]; // top 20 by coverage; fieldsTotal carries the real count\n  fieldsTotal: number;\n  features: { on: FeatureName[]; off: FeatureName[] };\n  hubs: Row[];\n  recent: Row[];\n}\n\nconst INTERNAL_COLUMNS = new Set(['path', '_mtime', '_size', '_rank']);\n\n// A result row is capped at SQLITE_MAX_COLUMN (2000, default); two aggregate expressions\n// per field keeps a chunk's row safely under that regardless of how many fields the tree has.\nconst MAP_COLUMN_CHUNK = 300;\n\nfunction chunk<T>(items: T[], size: number): T[][] {\n  const out: T[][] = [];\n  for (let i = 0; i < items.length; i += size) out.push(items.slice(i, i + size));\n  return out;\n}\n\n// Layer 0: what is this tree. Fixed-size output regardless of tree size.\nexport function mapTree(db: DatabaseSync, cfg: ResolvedConfig): TreeMap {\n  const docs = db.prepare('SELECT COUNT(*) AS count, COALESCE(SUM(\"_size\"), 0) AS bytes FROM frontmatter').get() as { count: number; bytes: number };\n\n  const columns = (db.prepare('PRAGMA table_info(frontmatter)').all() as Array<{ name: string }>).map((r) => r.name).filter((name) => !INTERNAL_COLUMNS.has(name));\n  // Observed storage class, not a declared one: these columns are added dynamically and\n  // SQLite types per value, so a field can be text in most notes and numeric in a few.\n  // Listing every distinct type makes both the type and any drift visible.\n  // One aggregate scan per chunk of columns rather than one scan per column: COUNT already\n  // ignores NULL, and FILTER keeps typeof() looking only at the non-null rows COUNT counted,\n  // matching the old per-column `WHERE ... IS NOT NULL` exactly.\n  const allFields: Row[] = [];\n  for (const group of chunk(columns, MAP_COLUMN_CHUNK)) {\n    const exprs = group.map((name, i) => {\n      const quoted = `\"${name.split('\"').join('\"\"')}\"`;\n      return `COUNT(${quoted}) AS n${i}, GROUP_CONCAT(DISTINCT typeof(${quoted})) FILTER (WHERE ${quoted} IS NOT NULL) AS t${i}`;\n    });\n    const result = db.prepare(`SELECT ${exprs.join(', ')} FROM frontmatter`).get() as Record<string, number | string | null>;\n    group.forEach((name, i) => allFields.push({ field: name, coverage: result[`n${i}`] as number, type: (result[`t${i}`] as string) ?? '' }));\n  }\n  allFields.sort((a, b) => (b.coverage as number) - (a.coverage as number));\n  const fields = allFields.slice(0, 20);\n\n  const hubs = featureEnabled(cfg, 'rank') ? (db.prepare(`SELECT f.\"path\" AS path, round(f.\"_rank\" * 100, 2) AS rank, content.title FROM frontmatter f JOIN content ON content.path = f.\"path\" WHERE f.\"_rank\" IS NOT NULL ORDER BY f.\"_rank\" DESC LIMIT 8`).all() as Row[]) : [];\n\n  const recent = db.prepare(`SELECT \"path\", datetime(\"_mtime\" / 1000, 'unixepoch') AS modified FROM frontmatter ORDER BY \"_mtime\" DESC LIMIT 5`).all() as Row[];\n\n  return { docs, fields, fieldsTotal: allFields.length, features: featureStates(cfg), hubs, recent };\n}\n\nexport interface Peek {\n  path: string;\n  tokens: number;\n  frontmatter: Row;\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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package/dist/esm/config.d.ts

@@ -10,6 +10,12 @@ export interface EmbedConfig {
     key?: string;
 }
 export declare const DEFAULT_EMBED_MODEL = "minishlab/potion-retrieval-32M";
+export interface SavedFind {
+    find: string;
+    k?: number;
+    where?: string;
+    semantic?: boolean;
+}
 export interface Config {
     $schema?: string;
     version?: number;
@@ -28,7 +34,7 @@ export interface Config {
         };
     };
     checks?: Record<string, 'empty'>;
-    queries: Record<string, string>;
+    queries: Record<string, string | SavedFind>;
 }
 export interface ResolvedConfig extends Config {
     baseDir: string;

package/dist/esm/config.js

@@ -5,7 +5,7 @@ export const CONFIG_FILENAME = 'sense.config.json';
 export const STATE_DIR = '.sense';
 // Highest sense.config.json `version` this build understands. Older versions auto-migrate on load.
 export const SUPPORTED_CONFIG_VERSION = 2;
-// Each feature owns its tables, parse-time extraction, and reconcile step; verbs degrade when one is off.
+// Each feature owns its tables, parse-time extraction, and reconcile step; commands degrade when one is off.
 // links/sections/rank are opt-out (absent = on); embed is opt-in (absent = off) -- most trees don't need vectors.
 const FEATURE_NAMES = [
     'links',
@@ -31,7 +31,7 @@ export function featureEnabled(cfg, name) {
 export function enabledFeatures(cfg) {
     return FEATURE_NAMES.filter((name)=>featureEnabled(cfg, name));
 }
-// Every feature with its current state; verbs surface this so "off" and "empty" stay
+// Every feature with its current state; commands surface this so "off" and "empty" stay
 // distinguishable in output.
 export function featureStates(cfg) {
     return {
@@ -154,6 +154,35 @@ function unknownConfigKeys(cfg) {
     }
     return unknown;
 }
+const SAVED_FIND_KEYS = new Set([
+    'find',
+    'k',
+    'where',
+    'semantic'
+]);
+// A queries.<name> entry that isn't a SQL string must be a saved find: { find, k?, where?, semantic? }.
+function validateSavedFind(name, value, configPath) {
+    if (typeof value !== 'object' || value === null || Array.isArray(value)) {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name} must be a SQL string or { find, k?, where?, semantic? }`);
+    }
+    const entry = value;
+    const unknown = Object.keys(entry).filter((k)=>!SAVED_FIND_KEYS.has(k));
+    if (unknown.length > 0) {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name} has unknown key(s) ${unknown.join(', ')}; a saved find takes find, k, where, semantic`);
+    }
+    if (typeof entry.find !== 'string') {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name}.find must be a string`);
+    }
+    if (entry.k !== undefined && (typeof entry.k !== 'number' || !Number.isInteger(entry.k) || entry.k <= 0)) {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name}.k must be a positive integer`);
+    }
+    if (entry.where !== undefined && typeof entry.where !== 'string') {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name}.where must be a SQL condition string`);
+    }
+    if (entry.semantic !== undefined && typeof entry.semantic !== 'boolean') {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries.${name}.semantic must be a boolean`);
+    }
+}
 function validateConfig(parsed, configPath) {
     var _cfg_features;
     var _defaults_find;
@@ -166,8 +195,12 @@ function validateConfig(parsed, configPath) {
         throw new SenseError('CONFIG_INVALID', `${configPath}: scan.include must be a non-empty array of glob strings`);
     }
     if (cfg.queries === undefined) cfg.queries = {};
-    if (typeof cfg.queries !== 'object' || cfg.queries === null || Array.isArray(cfg.queries) || !Object.values(cfg.queries).every((q)=>typeof q === 'string')) {
-        throw new SenseError('CONFIG_INVALID', `${configPath}: queries must be an object of name -> SQL string`);
+    if (typeof cfg.queries !== 'object' || cfg.queries === null || Array.isArray(cfg.queries)) {
+        throw new SenseError('CONFIG_INVALID', `${configPath}: queries must be an object of name -> SQL string or saved find`);
+    }
+    for (const [name, value] of Object.entries(cfg.queries)){
+        if (typeof value === 'string') continue;
+        validateSavedFind(name, value, configPath);
     }
     const defaults = cfg.defaults;
     if (defaults !== undefined && (typeof defaults !== 'object' || defaults === null || Array.isArray(defaults) || defaults.find !== undefined && typeof ((_defaults_find = defaults.find) === null || _defaults_find === void 0 ? void 0 : _defaults_find.where) !== 'string')) {
@@ -182,6 +215,7 @@ function validateConfig(parsed, configPath) {
         const queries = (_cfg_queries = cfg.queries) !== null && _cfg_queries !== void 0 ? _cfg_queries : {};
         for (const name of Object.keys(checks)){
             if (queries[name] === undefined) throw new SenseError('CONFIG_INVALID', `${configPath}: checks names "${name}", which is not a saved query`);
+            if (typeof queries[name] !== 'string') throw new SenseError('CONFIG_INVALID', `${configPath}: checks names "${name}", which is a saved find, not a SQL query`);
         }
     }
     if (cfg.features !== undefined && (typeof cfg.features !== 'object' || cfg.features === null || Array.isArray(cfg.features))) {