@tobilu/qmd 1.0.0 → 1.0.6

package/dist/store.js

@@ -0,0 +1,2374 @@
+/**
+ * QMD Store - Core data access and retrieval functions
+ *
+ * This module provides all database operations, search functions, and document
+ * retrieval for QMD. It returns raw data structures that can be formatted by
+ * CLI or MCP consumers.
+ *
+ * Usage:
+ *   const store = createStore("/path/to/db.sqlite");
+ *   // or use default path:
+ *   const store = createStore();
+ */
+import { openDatabase, loadSqliteVec } from "./db.js";
+import picomatch from "picomatch";
+import { createHash } from "crypto";
+import { realpathSync, statSync, mkdirSync } from "node:fs";
+import { LlamaCpp, getDefaultLlamaCpp, formatQueryForEmbedding, formatDocForEmbedding, } from "./llm.js";
+import { findContextForPath as collectionsFindContextForPath, addContext as collectionsAddContext, removeContext as collectionsRemoveContext, listAllContexts as collectionsListAllContexts, getCollection, listCollections as collectionsListCollections, addCollection as collectionsAddCollection, removeCollection as collectionsRemoveCollection, renameCollection as collectionsRenameCollection, setGlobalContext, loadConfig as collectionsLoadConfig, } from "./collections.js";
+// =============================================================================
+// Configuration
+// =============================================================================
+const HOME = process.env.HOME || "/tmp";
+export const DEFAULT_EMBED_MODEL = "embeddinggemma";
+export const DEFAULT_RERANK_MODEL = "ExpedientFalcon/qwen3-reranker:0.6b-q8_0";
+export const DEFAULT_QUERY_MODEL = "Qwen/Qwen3-1.7B";
+export const DEFAULT_GLOB = "**/*.md";
+export const DEFAULT_MULTI_GET_MAX_BYTES = 10 * 1024; // 10KB
+// Chunking: 900 tokens per chunk with 15% overlap
+// Increased from 800 to accommodate smart chunking finding natural break points
+export const CHUNK_SIZE_TOKENS = 900;
+export const CHUNK_OVERLAP_TOKENS = Math.floor(CHUNK_SIZE_TOKENS * 0.15); // 135 tokens (15% overlap)
+// Fallback char-based approximation for sync chunking (~4 chars per token)
+export const CHUNK_SIZE_CHARS = CHUNK_SIZE_TOKENS * 4; // 3600 chars
+export const CHUNK_OVERLAP_CHARS = CHUNK_OVERLAP_TOKENS * 4; // 540 chars
+// Search window for finding optimal break points (in tokens, ~200 tokens)
+export const CHUNK_WINDOW_TOKENS = 200;
+export const CHUNK_WINDOW_CHARS = CHUNK_WINDOW_TOKENS * 4; // 800 chars
+/**
+ * Patterns for detecting break points in markdown documents.
+ * Higher scores indicate better places to split.
+ * Scores are spread wide so headings decisively beat lower-quality breaks.
+ * Order matters for scoring - more specific patterns first.
+ */
+export const BREAK_PATTERNS = [
+    [/\n#{1}(?!#)/g, 100, 'h1'], // # but not ##
+    [/\n#{2}(?!#)/g, 90, 'h2'], // ## but not ###
+    [/\n#{3}(?!#)/g, 80, 'h3'], // ### but not ####
+    [/\n#{4}(?!#)/g, 70, 'h4'], // #### but not #####
+    [/\n#{5}(?!#)/g, 60, 'h5'], // ##### but not ######
+    [/\n#{6}(?!#)/g, 50, 'h6'], // ######
+    [/\n```/g, 80, 'codeblock'], // code block boundary (same as h3)
+    [/\n(?:---|\*\*\*|___)\s*\n/g, 60, 'hr'], // horizontal rule
+    [/\n\n+/g, 20, 'blank'], // paragraph boundary
+    [/\n[-*]\s/g, 5, 'list'], // unordered list item
+    [/\n\d+\.\s/g, 5, 'numlist'], // ordered list item
+    [/\n/g, 1, 'newline'], // minimal break
+];
+/**
+ * Scan text for all potential break points.
+ * Returns sorted array of break points with higher-scoring patterns taking precedence
+ * when multiple patterns match the same position.
+ */
+export function scanBreakPoints(text) {
+    const points = [];
+    const seen = new Map(); // pos -> best break point at that pos
+    for (const [pattern, score, type] of BREAK_PATTERNS) {
+        for (const match of text.matchAll(pattern)) {
+            const pos = match.index;
+            const existing = seen.get(pos);
+            // Keep higher score if position already seen
+            if (!existing || score > existing.score) {
+                const bp = { pos, score, type };
+                seen.set(pos, bp);
+            }
+        }
+    }
+    // Convert to array and sort by position
+    for (const bp of seen.values()) {
+        points.push(bp);
+    }
+    return points.sort((a, b) => a.pos - b.pos);
+}
+/**
+ * Find all code fence regions in the text.
+ * Code fences are delimited by ``` and we should never split inside them.
+ */
+export function findCodeFences(text) {
+    const regions = [];
+    const fencePattern = /\n```/g;
+    let inFence = false;
+    let fenceStart = 0;
+    for (const match of text.matchAll(fencePattern)) {
+        if (!inFence) {
+            fenceStart = match.index;
+            inFence = true;
+        }
+        else {
+            regions.push({ start: fenceStart, end: match.index + match[0].length });
+            inFence = false;
+        }
+    }
+    // Handle unclosed fence - extends to end of document
+    if (inFence) {
+        regions.push({ start: fenceStart, end: text.length });
+    }
+    return regions;
+}
+/**
+ * Check if a position is inside a code fence region.
+ */
+export function isInsideCodeFence(pos, fences) {
+    return fences.some(f => pos > f.start && pos < f.end);
+}
+/**
+ * Find the best cut position using scored break points with distance decay.
+ *
+ * Uses squared distance for gentler early decay - headings far back still win
+ * over low-quality breaks near the target.
+ *
+ * @param breakPoints - Pre-scanned break points from scanBreakPoints()
+ * @param targetCharPos - The ideal cut position (e.g., maxChars boundary)
+ * @param windowChars - How far back to search for break points (default ~200 tokens)
+ * @param decayFactor - How much to penalize distance (0.7 = 30% score at window edge)
+ * @param codeFences - Code fence regions to avoid splitting inside
+ * @returns The best position to cut at
+ */
+export function findBestCutoff(breakPoints, targetCharPos, windowChars = CHUNK_WINDOW_CHARS, decayFactor = 0.7, codeFences = []) {
+    const windowStart = targetCharPos - windowChars;
+    let bestScore = -1;
+    let bestPos = targetCharPos;
+    for (const bp of breakPoints) {
+        if (bp.pos < windowStart)
+            continue;
+        if (bp.pos > targetCharPos)
+            break; // sorted, so we can stop
+        // Skip break points inside code fences
+        if (isInsideCodeFence(bp.pos, codeFences))
+            continue;
+        const distance = targetCharPos - bp.pos;
+        // Squared distance decay: gentle early, steep late
+        // At target: multiplier = 1.0
+        // At 25% back: multiplier = 0.956
+        // At 50% back: multiplier = 0.825
+        // At 75% back: multiplier = 0.606
+        // At window edge: multiplier = 0.3
+        const normalizedDist = distance / windowChars;
+        const multiplier = 1.0 - (normalizedDist * normalizedDist) * decayFactor;
+        const finalScore = bp.score * multiplier;
+        if (finalScore > bestScore) {
+            bestScore = finalScore;
+            bestPos = bp.pos;
+        }
+    }
+    return bestPos;
+}
+// Hybrid query: strong BM25 signal detection thresholds
+// Skip expensive LLM expansion when top result is strong AND clearly separated from runner-up
+export const STRONG_SIGNAL_MIN_SCORE = 0.85;
+export const STRONG_SIGNAL_MIN_GAP = 0.15;
+// Max candidates to pass to reranker — balances quality vs latency.
+// 40 keeps rank 31-40 visible to the reranker (matters for recall on broad queries).
+export const RERANK_CANDIDATE_LIMIT = 40;
+// =============================================================================
+// Path utilities
+// =============================================================================
+export function homedir() {
+    return HOME;
+}
+/**
+ * Check if a path is absolute.
+ * Supports:
+ * - Unix paths: /path/to/file
+ * - Windows native: C:\path or C:/path
+ * - Git Bash: /c/path or /C/path (C-Z drives, excluding A/B floppy drives)
+ *
+ * Note: /c without trailing slash is treated as Unix path (directory named "c"),
+ * while /c/ or /c/path are treated as Git Bash paths (C: drive).
+ */
+export function isAbsolutePath(path) {
+    if (!path)
+        return false;
+    // Unix absolute path
+    if (path.startsWith('/')) {
+        // Check if it's a Git Bash style path like /c/ or /c/Users (C-Z only, not A or B)
+        // Requires path[2] === '/' to distinguish from Unix paths like /c or /cache
+        if (path.length >= 3 && path[2] === '/') {
+            const driveLetter = path[1];
+            if (driveLetter && /[c-zC-Z]/.test(driveLetter)) {
+                return true;
+            }
+        }
+        // Any other path starting with / is Unix absolute
+        return true;
+    }
+    // Windows native path: C:\ or C:/ (any letter A-Z)
+    if (path.length >= 2 && /[a-zA-Z]/.test(path[0]) && path[1] === ':') {
+        return true;
+    }
+    return false;
+}
+/**
+ * Normalize path separators to forward slashes.
+ * Converts Windows backslashes to forward slashes.
+ */
+export function normalizePathSeparators(path) {
+    return path.replace(/\\/g, '/');
+}
+/**
+ * Get the relative path from a prefix.
+ * Returns null if path is not under prefix.
+ * Returns empty string if path equals prefix.
+ */
+export function getRelativePathFromPrefix(path, prefix) {
+    // Empty prefix is invalid
+    if (!prefix) {
+        return null;
+    }
+    const normalizedPath = normalizePathSeparators(path);
+    const normalizedPrefix = normalizePathSeparators(prefix);
+    // Ensure prefix ends with / for proper matching
+    const prefixWithSlash = !normalizedPrefix.endsWith('/')
+        ? normalizedPrefix + '/'
+        : normalizedPrefix;
+    // Exact match
+    if (normalizedPath === normalizedPrefix) {
+        return '';
+    }
+    // Check if path starts with prefix
+    if (normalizedPath.startsWith(prefixWithSlash)) {
+        return normalizedPath.slice(prefixWithSlash.length);
+    }
+    return null;
+}
+export function resolve(...paths) {
+    if (paths.length === 0) {
+        throw new Error("resolve: at least one path segment is required");
+    }
+    // Normalize all paths to use forward slashes
+    const normalizedPaths = paths.map(normalizePathSeparators);
+    let result = '';
+    let windowsDrive = '';
+    // Check if first path is absolute
+    const firstPath = normalizedPaths[0];
+    if (isAbsolutePath(firstPath)) {
+        result = firstPath;
+        // Extract Windows drive letter if present
+        if (firstPath.length >= 2 && /[a-zA-Z]/.test(firstPath[0]) && firstPath[1] === ':') {
+            windowsDrive = firstPath.slice(0, 2);
+            result = firstPath.slice(2);
+        }
+        else if (firstPath.startsWith('/') && firstPath.length >= 3 && firstPath[2] === '/') {
+            // Git Bash style: /c/ -> C: (C-Z drives only, not A or B)
+            const driveLetter = firstPath[1];
+            if (driveLetter && /[c-zC-Z]/.test(driveLetter)) {
+                windowsDrive = driveLetter.toUpperCase() + ':';
+                result = firstPath.slice(2);
+            }
+        }
+    }
+    else {
+        // Start with PWD or cwd, then append the first relative path
+        const pwd = normalizePathSeparators(process.env.PWD || process.cwd());
+        // Extract Windows drive from PWD if present
+        if (pwd.length >= 2 && /[a-zA-Z]/.test(pwd[0]) && pwd[1] === ':') {
+            windowsDrive = pwd.slice(0, 2);
+            result = pwd.slice(2) + '/' + firstPath;
+        }
+        else {
+            result = pwd + '/' + firstPath;
+        }
+    }
+    // Process remaining paths
+    for (let i = 1; i < normalizedPaths.length; i++) {
+        const p = normalizedPaths[i];
+        if (isAbsolutePath(p)) {
+            // Absolute path replaces everything
+            result = p;
+            // Update Windows drive if present
+            if (p.length >= 2 && /[a-zA-Z]/.test(p[0]) && p[1] === ':') {
+                windowsDrive = p.slice(0, 2);
+                result = p.slice(2);
+            }
+            else if (p.startsWith('/') && p.length >= 3 && p[2] === '/') {
+                // Git Bash style (C-Z drives only, not A or B)
+                const driveLetter = p[1];
+                if (driveLetter && /[c-zC-Z]/.test(driveLetter)) {
+                    windowsDrive = driveLetter.toUpperCase() + ':';
+                    result = p.slice(2);
+                }
+                else {
+                    windowsDrive = '';
+                }
+            }
+            else {
+                windowsDrive = '';
+            }
+        }
+        else {
+            // Relative path - append
+            result = result + '/' + p;
+        }
+    }
+    // Normalize . and .. components
+    const parts = result.split('/').filter(Boolean);
+    const normalized = [];
+    for (const part of parts) {
+        if (part === '..') {
+            normalized.pop();
+        }
+        else if (part !== '.') {
+            normalized.push(part);
+        }
+    }
+    // Build final path
+    const finalPath = '/' + normalized.join('/');
+    // Prepend Windows drive if present
+    if (windowsDrive) {
+        return windowsDrive + finalPath;
+    }
+    return finalPath;
+}
+// Flag to indicate production mode (set by qmd.ts at startup)
+let _productionMode = false;
+export function enableProductionMode() {
+    _productionMode = true;
+}
+export function getDefaultDbPath(indexName = "index") {
+    // Always allow override via INDEX_PATH (for testing)
+    if (process.env.INDEX_PATH) {
+        return process.env.INDEX_PATH;
+    }
+    // In non-production mode (tests), require explicit path
+    if (!_productionMode) {
+        throw new Error("Database path not set. Tests must set INDEX_PATH env var or use createStore() with explicit path. " +
+            "This prevents tests from accidentally writing to the global index.");
+    }
+    const cacheDir = process.env.XDG_CACHE_HOME || resolve(homedir(), ".cache");
+    const qmdCacheDir = resolve(cacheDir, "qmd");
+    try {
+        mkdirSync(qmdCacheDir, { recursive: true });
+    }
+    catch { }
+    return resolve(qmdCacheDir, `${indexName}.sqlite`);
+}
+export function getPwd() {
+    return process.env.PWD || process.cwd();
+}
+export function getRealPath(path) {
+    try {
+        return realpathSync(path);
+    }
+    catch {
+        return resolve(path);
+    }
+}
+/**
+ * Normalize explicit virtual path formats to standard qmd:// format.
+ * Only handles paths that are already explicitly virtual:
+ * - qmd://collection/path.md (already normalized)
+ * - qmd:////collection/path.md (extra slashes - normalize)
+ * - //collection/path.md (missing qmd: prefix - add it)
+ *
+ * Does NOT handle:
+ * - collection/path.md (bare paths - could be filesystem relative)
+ * - :linenum suffix (should be parsed separately before calling this)
+ */
+export function normalizeVirtualPath(input) {
+    let path = input.trim();
+    // Handle qmd:// with extra slashes: qmd:////collection/path -> qmd://collection/path
+    if (path.startsWith('qmd:')) {
+        // Remove qmd: prefix and normalize slashes
+        path = path.slice(4);
+        // Remove leading slashes and re-add exactly two
+        path = path.replace(/^\/+/, '');
+        return `qmd://${path}`;
+    }
+    // Handle //collection/path (missing qmd: prefix)
+    if (path.startsWith('//')) {
+        path = path.replace(/^\/+/, '');
+        return `qmd://${path}`;
+    }
+    // Return as-is for other cases (filesystem paths, docids, bare collection/path, etc.)
+    return path;
+}
+/**
+ * Parse a virtual path like "qmd://collection-name/path/to/file.md"
+ * into its components.
+ * Also supports collection root: "qmd://collection-name/" or "qmd://collection-name"
+ */
+export function parseVirtualPath(virtualPath) {
+    // Normalize the path first
+    const normalized = normalizeVirtualPath(virtualPath);
+    // Match: qmd://collection-name[/optional-path]
+    // Allows: qmd://name, qmd://name/, qmd://name/path
+    const match = normalized.match(/^qmd:\/\/([^\/]+)\/?(.*)$/);
+    if (!match?.[1])
+        return null;
+    return {
+        collectionName: match[1],
+        path: match[2] ?? '', // Empty string for collection root
+    };
+}
+/**
+ * Build a virtual path from collection name and relative path.
+ */
+export function buildVirtualPath(collectionName, path) {
+    return `qmd://${collectionName}/${path}`;
+}
+/**
+ * Check if a path is explicitly a virtual path.
+ * Only recognizes explicit virtual path formats:
+ * - qmd://collection/path.md
+ * - //collection/path.md
+ *
+ * Does NOT consider bare collection/path.md as virtual - that should be
+ * handled separately by checking if the first component is a collection name.
+ */
+export function isVirtualPath(path) {
+    const trimmed = path.trim();
+    // Explicit qmd:// prefix (with any number of slashes)
+    if (trimmed.startsWith('qmd:'))
+        return true;
+    // //collection/path format (missing qmd: prefix)
+    if (trimmed.startsWith('//'))
+        return true;
+    return false;
+}
+/**
+ * Resolve a virtual path to absolute filesystem path.
+ */
+export function resolveVirtualPath(db, virtualPath) {
+    const parsed = parseVirtualPath(virtualPath);
+    if (!parsed)
+        return null;
+    const coll = getCollectionByName(db, parsed.collectionName);
+    if (!coll)
+        return null;
+    return resolve(coll.pwd, parsed.path);
+}
+/**
+ * Convert an absolute filesystem path to a virtual path.
+ * Returns null if the file is not in any indexed collection.
+ */
+export function toVirtualPath(db, absolutePath) {
+    // Get all collections from YAML config
+    const collections = collectionsListCollections();
+    // Find which collection this absolute path belongs to
+    for (const coll of collections) {
+        if (absolutePath.startsWith(coll.path + '/') || absolutePath === coll.path) {
+            // Extract relative path
+            const relativePath = absolutePath.startsWith(coll.path + '/')
+                ? absolutePath.slice(coll.path.length + 1)
+                : '';
+            // Verify this document exists in the database
+            const doc = db.prepare(`
+        SELECT d.path
+        FROM documents d
+        WHERE d.collection = ? AND d.path = ? AND d.active = 1
+        LIMIT 1
+      `).get(coll.name, relativePath);
+            if (doc) {
+                return buildVirtualPath(coll.name, relativePath);
+            }
+        }
+    }
+    return null;
+}
+// =============================================================================
+// Database initialization
+// =============================================================================
+function createSqliteVecUnavailableError(reason) {
+    return new Error("sqlite-vec extension is unavailable. " +
+        `${reason}. ` +
+        "Install Homebrew SQLite so the sqlite-vec extension can be loaded, " +
+        "and set BREW_PREFIX if Homebrew is installed in a non-standard location.");
+}
+function getErrorMessage(err) {
+    return err instanceof Error ? err.message : String(err);
+}
+export function verifySqliteVecLoaded(db) {
+    try {
+        const row = db.prepare(`SELECT vec_version() AS version`).get();
+        if (!row?.version || typeof row.version !== "string") {
+            throw new Error("vec_version() returned no version");
+        }
+    }
+    catch (err) {
+        const message = getErrorMessage(err);
+        throw createSqliteVecUnavailableError(`sqlite-vec probe failed (${message})`);
+    }
+}
+let _sqliteVecAvailable = null;
+function initializeDatabase(db) {
+    try {
+        loadSqliteVec(db);
+        verifySqliteVecLoaded(db);
+        _sqliteVecAvailable = true;
+    }
+    catch {
+        // sqlite-vec is optional — vector search won't work but FTS is fine
+        _sqliteVecAvailable = false;
+    }
+    db.exec("PRAGMA journal_mode = WAL");
+    db.exec("PRAGMA foreign_keys = ON");
+    // Drop legacy tables that are now managed in YAML
+    db.exec(`DROP TABLE IF EXISTS path_contexts`);
+    db.exec(`DROP TABLE IF EXISTS collections`);
+    // Content-addressable storage - the source of truth for document content
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS content (
+      hash TEXT PRIMARY KEY,
+      doc TEXT NOT NULL,
+      created_at TEXT NOT NULL
+    )
+  `);
+    // Documents table - file system layer mapping virtual paths to content hashes
+    // Collections are now managed in ~/.config/qmd/index.yml
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS documents (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      collection TEXT NOT NULL,
+      path TEXT NOT NULL,
+      title TEXT NOT NULL,
+      hash TEXT NOT NULL,
+      created_at TEXT NOT NULL,
+      modified_at TEXT NOT NULL,
+      active INTEGER NOT NULL DEFAULT 1,
+      FOREIGN KEY (hash) REFERENCES content(hash) ON DELETE CASCADE,
+      UNIQUE(collection, path)
+    )
+  `);
+    db.exec(`CREATE INDEX IF NOT EXISTS idx_documents_collection ON documents(collection, active)`);
+    db.exec(`CREATE INDEX IF NOT EXISTS idx_documents_hash ON documents(hash)`);
+    db.exec(`CREATE INDEX IF NOT EXISTS idx_documents_path ON documents(path, active)`);
+    // Cache table for LLM API calls
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS llm_cache (
+      hash TEXT PRIMARY KEY,
+      result TEXT NOT NULL,
+      created_at TEXT NOT NULL
+    )
+  `);
+    // Content vectors
+    const cvInfo = db.prepare(`PRAGMA table_info(content_vectors)`).all();
+    const hasSeqColumn = cvInfo.some(col => col.name === 'seq');
+    if (cvInfo.length > 0 && !hasSeqColumn) {
+        db.exec(`DROP TABLE IF EXISTS content_vectors`);
+        db.exec(`DROP TABLE IF EXISTS vectors_vec`);
+    }
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS content_vectors (
+      hash TEXT NOT NULL,
+      seq INTEGER NOT NULL DEFAULT 0,
+      pos INTEGER NOT NULL DEFAULT 0,
+      model TEXT NOT NULL,
+      embedded_at TEXT NOT NULL,
+      PRIMARY KEY (hash, seq)
+    )
+  `);
+    // FTS - index filepath (collection/path), title, and content
+    db.exec(`
+    CREATE VIRTUAL TABLE IF NOT EXISTS documents_fts USING fts5(
+      filepath, title, body,
+      tokenize='porter unicode61'
+    )
+  `);
+    // Triggers to keep FTS in sync
+    db.exec(`
+    CREATE TRIGGER IF NOT EXISTS documents_ai AFTER INSERT ON documents
+    WHEN new.active = 1
+    BEGIN
+      INSERT INTO documents_fts(rowid, filepath, title, body)
+      SELECT
+        new.id,
+        new.collection || '/' || new.path,
+        new.title,
+        (SELECT doc FROM content WHERE hash = new.hash)
+      WHERE new.active = 1;
+    END
+  `);
+    db.exec(`
+    CREATE TRIGGER IF NOT EXISTS documents_ad AFTER DELETE ON documents BEGIN
+      DELETE FROM documents_fts WHERE rowid = old.id;
+    END
+  `);
+    db.exec(`
+    CREATE TRIGGER IF NOT EXISTS documents_au AFTER UPDATE ON documents
+    BEGIN
+      -- Delete from FTS if no longer active
+      DELETE FROM documents_fts WHERE rowid = old.id AND new.active = 0;
+
+      -- Update FTS if still/newly active
+      INSERT OR REPLACE INTO documents_fts(rowid, filepath, title, body)
+      SELECT
+        new.id,
+        new.collection || '/' || new.path,
+        new.title,
+        (SELECT doc FROM content WHERE hash = new.hash)
+      WHERE new.active = 1;
+    END
+  `);
+}
+export function isSqliteVecAvailable() {
+    return _sqliteVecAvailable === true;
+}
+function ensureVecTableInternal(db, dimensions) {
+    if (!_sqliteVecAvailable) {
+        throw new Error("sqlite-vec is not available. Vector operations require a SQLite build with extension loading support.");
+    }
+    const tableInfo = db.prepare(`SELECT sql FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    if (tableInfo) {
+        const match = tableInfo.sql.match(/float\[(\d+)\]/);
+        const hasHashSeq = tableInfo.sql.includes('hash_seq');
+        const hasCosine = tableInfo.sql.includes('distance_metric=cosine');
+        const existingDims = match?.[1] ? parseInt(match[1], 10) : null;
+        if (existingDims === dimensions && hasHashSeq && hasCosine)
+            return;
+        // Table exists but wrong schema - need to rebuild
+        db.exec("DROP TABLE IF EXISTS vectors_vec");
+    }
+    db.exec(`CREATE VIRTUAL TABLE vectors_vec USING vec0(hash_seq TEXT PRIMARY KEY, embedding float[${dimensions}] distance_metric=cosine)`);
+}
+/**
+ * Create a new store instance with the given database path.
+ * If no path is provided, uses the default path (~/.cache/qmd/index.sqlite).
+ *
+ * @param dbPath - Path to the SQLite database file
+ * @returns Store instance with all methods bound to the database
+ */
+export function createStore(dbPath) {
+    const resolvedPath = dbPath || getDefaultDbPath();
+    const db = openDatabase(resolvedPath);
+    initializeDatabase(db);
+    return {
+        db,
+        dbPath: resolvedPath,
+        close: () => db.close(),
+        ensureVecTable: (dimensions) => ensureVecTableInternal(db, dimensions),
+        // Index health
+        getHashesNeedingEmbedding: () => getHashesNeedingEmbedding(db),
+        getIndexHealth: () => getIndexHealth(db),
+        getStatus: () => getStatus(db),
+        // Caching
+        getCacheKey,
+        getCachedResult: (cacheKey) => getCachedResult(db, cacheKey),
+        setCachedResult: (cacheKey, result) => setCachedResult(db, cacheKey, result),
+        clearCache: () => clearCache(db),
+        // Cleanup and maintenance
+        deleteLLMCache: () => deleteLLMCache(db),
+        deleteInactiveDocuments: () => deleteInactiveDocuments(db),
+        cleanupOrphanedContent: () => cleanupOrphanedContent(db),
+        cleanupOrphanedVectors: () => cleanupOrphanedVectors(db),
+        vacuumDatabase: () => vacuumDatabase(db),
+        // Context
+        getContextForFile: (filepath) => getContextForFile(db, filepath),
+        getContextForPath: (collectionName, path) => getContextForPath(db, collectionName, path),
+        getCollectionByName: (name) => getCollectionByName(db, name),
+        getCollectionsWithoutContext: () => getCollectionsWithoutContext(db),
+        getTopLevelPathsWithoutContext: (collectionName) => getTopLevelPathsWithoutContext(db, collectionName),
+        // Virtual paths
+        parseVirtualPath,
+        buildVirtualPath,
+        isVirtualPath,
+        resolveVirtualPath: (virtualPath) => resolveVirtualPath(db, virtualPath),
+        toVirtualPath: (absolutePath) => toVirtualPath(db, absolutePath),
+        // Search
+        searchFTS: (query, limit, collectionName) => searchFTS(db, query, limit, collectionName),
+        searchVec: (query, model, limit, collectionName, session, precomputedEmbedding) => searchVec(db, query, model, limit, collectionName, session, precomputedEmbedding),
+        // Query expansion & reranking
+        expandQuery: (query, model) => expandQuery(query, model, db),
+        rerank: (query, documents, model) => rerank(query, documents, model, db),
+        // Document retrieval
+        findDocument: (filename, options) => findDocument(db, filename, options),
+        getDocumentBody: (doc, fromLine, maxLines) => getDocumentBody(db, doc, fromLine, maxLines),
+        findDocuments: (pattern, options) => findDocuments(db, pattern, options),
+        // Fuzzy matching and docid lookup
+        findSimilarFiles: (query, maxDistance, limit) => findSimilarFiles(db, query, maxDistance, limit),
+        matchFilesByGlob: (pattern) => matchFilesByGlob(db, pattern),
+        findDocumentByDocid: (docid) => findDocumentByDocid(db, docid),
+        // Document indexing operations
+        insertContent: (hash, content, createdAt) => insertContent(db, hash, content, createdAt),
+        insertDocument: (collectionName, path, title, hash, createdAt, modifiedAt) => insertDocument(db, collectionName, path, title, hash, createdAt, modifiedAt),
+        findActiveDocument: (collectionName, path) => findActiveDocument(db, collectionName, path),
+        updateDocumentTitle: (documentId, title, modifiedAt) => updateDocumentTitle(db, documentId, title, modifiedAt),
+        updateDocument: (documentId, title, hash, modifiedAt) => updateDocument(db, documentId, title, hash, modifiedAt),
+        deactivateDocument: (collectionName, path) => deactivateDocument(db, collectionName, path),
+        getActiveDocumentPaths: (collectionName) => getActiveDocumentPaths(db, collectionName),
+        // Vector/embedding operations
+        getHashesForEmbedding: () => getHashesForEmbedding(db),
+        clearAllEmbeddings: () => clearAllEmbeddings(db),
+        insertEmbedding: (hash, seq, pos, embedding, model, embeddedAt) => insertEmbedding(db, hash, seq, pos, embedding, model, embeddedAt),
+    };
+}
+/**
+ * Extract short docid from a full hash (first 6 characters).
+ */
+export function getDocid(hash) {
+    return hash.slice(0, 6);
+}
+/**
+ * Handelize a filename to be more token-friendly.
+ * - Convert triple underscore `___` to `/` (folder separator)
+ * - Convert to lowercase
+ * - Replace sequences of non-word chars (except /) with single dash
+ * - Remove leading/trailing dashes from path segments
+ * - Preserve folder structure (a/b/c/d.md stays structured)
+ * - Preserve file extension
+ */
+export function handelize(path) {
+    if (!path || path.trim() === '') {
+        throw new Error('handelize: path cannot be empty');
+    }
+    // Allow route-style "$" filenames while still rejecting paths with no usable content.
+    const segments = path.split('/').filter(Boolean);
+    const lastSegment = segments[segments.length - 1] || '';
+    const filenameWithoutExt = lastSegment.replace(/\.[^.]+$/, '');
+    const hasValidContent = /[\p{L}\p{N}$]/u.test(filenameWithoutExt);
+    if (!hasValidContent) {
+        throw new Error(`handelize: path "${path}" has no valid filename content`);
+    }
+    const result = path
+        .replace(/___/g, '/') // Triple underscore becomes folder separator
+        .toLowerCase()
+        .split('/')
+        .map((segment, idx, arr) => {
+        const isLastSegment = idx === arr.length - 1;
+        if (isLastSegment) {
+            // For the filename (last segment), preserve the extension
+            const extMatch = segment.match(/(\.[a-z0-9]+)$/i);
+            const ext = extMatch ? extMatch[1] : '';
+            const nameWithoutExt = ext ? segment.slice(0, -ext.length) : segment;
+            const cleanedName = nameWithoutExt
+                .replace(/[^\p{L}\p{N}$]+/gu, '-') // Keep route marker "$", dash-separate other chars
+                .replace(/^-+|-+$/g, ''); // Remove leading/trailing dashes
+            return cleanedName + ext;
+        }
+        else {
+            // For directories, just clean normally
+            return segment
+                .replace(/[^\p{L}\p{N}$]+/gu, '-')
+                .replace(/^-+|-+$/g, '');
+        }
+    })
+        .filter(Boolean)
+        .join('/');
+    if (!result) {
+        throw new Error(`handelize: path "${path}" resulted in empty string after processing`);
+    }
+    return result;
+}
+// =============================================================================
+// Index health
+// =============================================================================
+export function getHashesNeedingEmbedding(db) {
+    const result = db.prepare(`
+    SELECT COUNT(DISTINCT d.hash) as count
+    FROM documents d
+    LEFT JOIN content_vectors v ON d.hash = v.hash AND v.seq = 0
+    WHERE d.active = 1 AND v.hash IS NULL
+  `).get();
+    return result.count;
+}
+export function getIndexHealth(db) {
+    const needsEmbedding = getHashesNeedingEmbedding(db);
+    const totalDocs = db.prepare(`SELECT COUNT(*) as count FROM documents WHERE active = 1`).get().count;
+    const mostRecent = db.prepare(`SELECT MAX(modified_at) as latest FROM documents WHERE active = 1`).get();
+    let daysStale = null;
+    if (mostRecent?.latest) {
+        const lastUpdate = new Date(mostRecent.latest);
+        daysStale = Math.floor((Date.now() - lastUpdate.getTime()) / (24 * 60 * 60 * 1000));
+    }
+    return { needsEmbedding, totalDocs, daysStale };
+}
+// =============================================================================
+// Caching
+// =============================================================================
+export function getCacheKey(url, body) {
+    const hash = createHash("sha256");
+    hash.update(url);
+    hash.update(JSON.stringify(body));
+    return hash.digest("hex");
+}
+export function getCachedResult(db, cacheKey) {
+    const row = db.prepare(`SELECT result FROM llm_cache WHERE hash = ?`).get(cacheKey);
+    return row?.result || null;
+}
+export function setCachedResult(db, cacheKey, result) {
+    const now = new Date().toISOString();
+    db.prepare(`INSERT OR REPLACE INTO llm_cache (hash, result, created_at) VALUES (?, ?, ?)`).run(cacheKey, result, now);
+    if (Math.random() < 0.01) {
+        db.exec(`DELETE FROM llm_cache WHERE hash NOT IN (SELECT hash FROM llm_cache ORDER BY created_at DESC LIMIT 1000)`);
+    }
+}
+export function clearCache(db) {
+    db.exec(`DELETE FROM llm_cache`);
+}
+// =============================================================================
+// Cleanup and maintenance operations
+// =============================================================================
+/**
+ * Delete cached LLM API responses.
+ * Returns the number of cached responses deleted.
+ */
+export function deleteLLMCache(db) {
+    const result = db.prepare(`DELETE FROM llm_cache`).run();
+    return result.changes;
+}
+/**
+ * Remove inactive document records (active = 0).
+ * Returns the number of inactive documents deleted.
+ */
+export function deleteInactiveDocuments(db) {
+    const result = db.prepare(`DELETE FROM documents WHERE active = 0`).run();
+    return result.changes;
+}
+/**
+ * Remove orphaned content hashes that are not referenced by any active document.
+ * Returns the number of orphaned content hashes deleted.
+ */
+export function cleanupOrphanedContent(db) {
+    const result = db.prepare(`
+    DELETE FROM content
+    WHERE hash NOT IN (SELECT DISTINCT hash FROM documents WHERE active = 1)
+  `).run();
+    return result.changes;
+}
+/**
+ * Remove orphaned vector embeddings that are not referenced by any active document.
+ * Returns the number of orphaned embedding chunks deleted.
+ */
+export function cleanupOrphanedVectors(db) {
+    // Check if vectors_vec table exists
+    const tableExists = db.prepare(`
+    SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'
+  `).get();
+    if (!tableExists) {
+        return 0;
+    }
+    // Count orphaned vectors first
+    const countResult = db.prepare(`
+    SELECT COUNT(*) as c FROM content_vectors cv
+    WHERE NOT EXISTS (
+      SELECT 1 FROM documents d WHERE d.hash = cv.hash AND d.active = 1
+    )
+  `).get();
+    if (countResult.c === 0) {
+        return 0;
+    }
+    // Delete from vectors_vec first
+    db.exec(`
+    DELETE FROM vectors_vec WHERE hash_seq IN (
+      SELECT cv.hash || '_' || cv.seq FROM content_vectors cv
+      WHERE NOT EXISTS (
+        SELECT 1 FROM documents d WHERE d.hash = cv.hash AND d.active = 1
+      )
+    )
+  `);
+    // Delete from content_vectors
+    db.exec(`
+    DELETE FROM content_vectors WHERE hash NOT IN (
+      SELECT hash FROM documents WHERE active = 1
+    )
+  `);
+    return countResult.c;
+}
+/**
+ * Run VACUUM to reclaim unused space in the database.
+ * This operation rebuilds the database file to eliminate fragmentation.
+ */
+export function vacuumDatabase(db) {
+    db.exec(`VACUUM`);
+}
+// =============================================================================
+// Document helpers
+// =============================================================================
+export async function hashContent(content) {
+    const hash = createHash("sha256");
+    hash.update(content);
+    return hash.digest("hex");
+}
+const titleExtractors = {
+    '.md': (content) => {
+        const match = content.match(/^##?\s+(.+)$/m);
+        if (match) {
+            const title = (match[1] ?? "").trim();
+            if (title === "📝 Notes" || title === "Notes") {
+                const nextMatch = content.match(/^##\s+(.+)$/m);
+                if (nextMatch?.[1])
+                    return nextMatch[1].trim();
+            }
+            return title;
+        }
+        return null;
+    },
+    '.org': (content) => {
+        const titleProp = content.match(/^#\+TITLE:\s*(.+)$/im);
+        if (titleProp?.[1])
+            return titleProp[1].trim();
+        const heading = content.match(/^\*+\s+(.+)$/m);
+        if (heading?.[1])
+            return heading[1].trim();
+        return null;
+    },
+};
+export function extractTitle(content, filename) {
+    const ext = filename.slice(filename.lastIndexOf('.')).toLowerCase();
+    const extractor = titleExtractors[ext];
+    if (extractor) {
+        const title = extractor(content);
+        if (title)
+            return title;
+    }
+    return filename.replace(/\.[^.]+$/, "").split("/").pop() || filename;
+}
+// =============================================================================
+// Document indexing operations
+// =============================================================================
+/**
+ * Insert content into the content table (content-addressable storage).
+ * Uses INSERT OR IGNORE so duplicate hashes are skipped.
+ */
+export function insertContent(db, hash, content, createdAt) {
+    db.prepare(`INSERT OR IGNORE INTO content (hash, doc, created_at) VALUES (?, ?, ?)`)
+        .run(hash, content, createdAt);
+}
+/**
+ * Insert a new document into the documents table.
+ */
+export function insertDocument(db, collectionName, path, title, hash, createdAt, modifiedAt) {
+    db.prepare(`
+    INSERT INTO documents (collection, path, title, hash, created_at, modified_at, active)
+    VALUES (?, ?, ?, ?, ?, ?, 1)
+    ON CONFLICT(collection, path) DO UPDATE SET
+      title = excluded.title,
+      hash = excluded.hash,
+      modified_at = excluded.modified_at,
+      active = 1
+  `).run(collectionName, path, title, hash, createdAt, modifiedAt);
+}
+/**
+ * Find an active document by collection name and path.
+ */
+export function findActiveDocument(db, collectionName, path) {
+    const row = db.prepare(`
+    SELECT id, hash, title FROM documents
+    WHERE collection = ? AND path = ? AND active = 1
+  `).get(collectionName, path);
+    return row ?? null;
+}
+/**
+ * Update the title and modified_at timestamp for a document.
+ */
+export function updateDocumentTitle(db, documentId, title, modifiedAt) {
+    db.prepare(`UPDATE documents SET title = ?, modified_at = ? WHERE id = ?`)
+        .run(title, modifiedAt, documentId);
+}
+/**
+ * Update an existing document's hash, title, and modified_at timestamp.
+ * Used when content changes but the file path stays the same.
+ */
+export function updateDocument(db, documentId, title, hash, modifiedAt) {
+    db.prepare(`UPDATE documents SET title = ?, hash = ?, modified_at = ? WHERE id = ?`)
+        .run(title, hash, modifiedAt, documentId);
+}
+/**
+ * Deactivate a document (mark as inactive but don't delete).
+ */
+export function deactivateDocument(db, collectionName, path) {
+    db.prepare(`UPDATE documents SET active = 0 WHERE collection = ? AND path = ? AND active = 1`)
+        .run(collectionName, path);
+}
+/**
+ * Get all active document paths for a collection.
+ */
+export function getActiveDocumentPaths(db, collectionName) {
+    const rows = db.prepare(`
+    SELECT path FROM documents WHERE collection = ? AND active = 1
+  `).all(collectionName);
+    return rows.map(r => r.path);
+}
+export { formatQueryForEmbedding, formatDocForEmbedding };
+export function chunkDocument(content, maxChars = CHUNK_SIZE_CHARS, overlapChars = CHUNK_OVERLAP_CHARS, windowChars = CHUNK_WINDOW_CHARS) {
+    if (content.length <= maxChars) {
+        return [{ text: content, pos: 0 }];
+    }
+    // Pre-scan all break points and code fences once
+    const breakPoints = scanBreakPoints(content);
+    const codeFences = findCodeFences(content);
+    const chunks = [];
+    let charPos = 0;
+    while (charPos < content.length) {
+        // Calculate target end position for this chunk
+        const targetEndPos = Math.min(charPos + maxChars, content.length);
+        let endPos = targetEndPos;
+        // If not at the end, find the best break point
+        if (endPos < content.length) {
+            // Find best cutoff using scored algorithm
+            const bestCutoff = findBestCutoff(breakPoints, targetEndPos, windowChars, 0.7, codeFences);
+            // Only use the cutoff if it's within our current chunk
+            if (bestCutoff > charPos && bestCutoff <= targetEndPos) {
+                endPos = bestCutoff;
+            }
+        }
+        // Ensure we make progress
+        if (endPos <= charPos) {
+            endPos = Math.min(charPos + maxChars, content.length);
+        }
+        chunks.push({ text: content.slice(charPos, endPos), pos: charPos });
+        // Move forward, but overlap with previous chunk
+        // For last chunk, don't overlap (just go to the end)
+        if (endPos >= content.length) {
+            break;
+        }
+        charPos = endPos - overlapChars;
+        const lastChunkPos = chunks.at(-1).pos;
+        if (charPos <= lastChunkPos) {
+            // Prevent infinite loop - move forward at least a bit
+            charPos = endPos;
+        }
+    }
+    return chunks;
+}
+/**
+ * Chunk a document by actual token count using the LLM tokenizer.
+ * More accurate than character-based chunking but requires async.
+ */
+export async function chunkDocumentByTokens(content, maxTokens = CHUNK_SIZE_TOKENS, overlapTokens = CHUNK_OVERLAP_TOKENS, windowTokens = CHUNK_WINDOW_TOKENS) {
+    const llm = getDefaultLlamaCpp();
+    // Use moderate chars/token estimate (prose ~4, code ~2, mixed ~3)
+    // If chunks exceed limit, they'll be re-split with actual ratio
+    const avgCharsPerToken = 3;
+    const maxChars = maxTokens * avgCharsPerToken;
+    const overlapChars = overlapTokens * avgCharsPerToken;
+    const windowChars = windowTokens * avgCharsPerToken;
+    // Chunk in character space with conservative estimate
+    let charChunks = chunkDocument(content, maxChars, overlapChars, windowChars);
+    // Tokenize and split any chunks that still exceed limit
+    const results = [];
+    for (const chunk of charChunks) {
+        const tokens = await llm.tokenize(chunk.text);
+        if (tokens.length <= maxTokens) {
+            results.push({ text: chunk.text, pos: chunk.pos, tokens: tokens.length });
+        }
+        else {
+            // Chunk is still too large - split it further
+            // Use actual token count to estimate better char limit
+            const actualCharsPerToken = chunk.text.length / tokens.length;
+            const safeMaxChars = Math.floor(maxTokens * actualCharsPerToken * 0.95); // 5% safety margin
+            const subChunks = chunkDocument(chunk.text, safeMaxChars, Math.floor(overlapChars * actualCharsPerToken / 2), Math.floor(windowChars * actualCharsPerToken / 2));
+            for (const subChunk of subChunks) {
+                const subTokens = await llm.tokenize(subChunk.text);
+                results.push({
+                    text: subChunk.text,
+                    pos: chunk.pos + subChunk.pos,
+                    tokens: subTokens.length,
+                });
+            }
+        }
+    }
+    return results;
+}
+// =============================================================================
+// Fuzzy matching
+// =============================================================================
+function levenshtein(a, b) {
+    const m = a.length, n = b.length;
+    if (m === 0)
+        return n;
+    if (n === 0)
+        return m;
+    const dp = Array.from({ length: m + 1 }, () => Array(n + 1).fill(0));
+    for (let i = 0; i <= m; i++)
+        dp[i][0] = i;
+    for (let j = 0; j <= n; j++)
+        dp[0][j] = j;
+    for (let i = 1; i <= m; i++) {
+        for (let j = 1; j <= n; j++) {
+            const cost = a[i - 1] === b[j - 1] ? 0 : 1;
+            dp[i][j] = Math.min(dp[i - 1][j] + 1, dp[i][j - 1] + 1, dp[i - 1][j - 1] + cost);
+        }
+    }
+    return dp[m][n];
+}
+/**
+ * Normalize a docid input by stripping surrounding quotes and leading #.
+ * Handles: "#abc123", 'abc123', "abc123", #abc123, abc123
+ * Returns the bare hex string.
+ */
+export function normalizeDocid(docid) {
+    let normalized = docid.trim();
+    // Strip surrounding quotes (single or double)
+    if ((normalized.startsWith('"') && normalized.endsWith('"')) ||
+        (normalized.startsWith("'") && normalized.endsWith("'"))) {
+        normalized = normalized.slice(1, -1);
+    }
+    // Strip leading # if present
+    if (normalized.startsWith('#')) {
+        normalized = normalized.slice(1);
+    }
+    return normalized;
+}
+/**
+ * Check if a string looks like a docid reference.
+ * Accepts: #abc123, abc123, "#abc123", "abc123", '#abc123', 'abc123'
+ * Returns true if the normalized form is a valid hex string of 6+ chars.
+ */
+export function isDocid(input) {
+    const normalized = normalizeDocid(input);
+    // Must be at least 6 hex characters
+    return normalized.length >= 6 && /^[a-f0-9]+$/i.test(normalized);
+}
+/**
+ * Find a document by its short docid (first 6 characters of hash).
+ * Returns the document's virtual path if found, null otherwise.
+ * If multiple documents match the same short hash (collision), returns the first one.
+ *
+ * Accepts lenient input: #abc123, abc123, "#abc123", "abc123"
+ */
+export function findDocumentByDocid(db, docid) {
+    const shortHash = normalizeDocid(docid);
+    if (shortHash.length < 1)
+        return null;
+    // Look up documents where hash starts with the short hash
+    const doc = db.prepare(`
+    SELECT 'qmd://' || d.collection || '/' || d.path as filepath, d.hash
+    FROM documents d
+    WHERE d.hash LIKE ? AND d.active = 1
+    LIMIT 1
+  `).get(`${shortHash}%`);
+    return doc;
+}
+export function findSimilarFiles(db, query, maxDistance = 3, limit = 5) {
+    const allFiles = db.prepare(`
+    SELECT d.path
+    FROM documents d
+    WHERE d.active = 1
+  `).all();
+    const queryLower = query.toLowerCase();
+    const scored = allFiles
+        .map(f => ({ path: f.path, dist: levenshtein(f.path.toLowerCase(), queryLower) }))
+        .filter(f => f.dist <= maxDistance)
+        .sort((a, b) => a.dist - b.dist)
+        .slice(0, limit);
+    return scored.map(f => f.path);
+}
+export function matchFilesByGlob(db, pattern) {
+    const allFiles = db.prepare(`
+    SELECT
+      'qmd://' || d.collection || '/' || d.path as virtual_path,
+      LENGTH(content.doc) as body_length,
+      d.path,
+      d.collection
+    FROM documents d
+    JOIN content ON content.hash = d.hash
+    WHERE d.active = 1
+  `).all();
+    const isMatch = picomatch(pattern);
+    return allFiles
+        .filter(f => isMatch(f.virtual_path) || isMatch(f.path))
+        .map(f => ({
+        filepath: f.virtual_path, // Virtual path for precise lookup
+        displayPath: f.path, // Relative path for display
+        bodyLength: f.body_length
+    }));
+}
+// =============================================================================
+// Context
+// =============================================================================
+/**
+ * Get context for a file path using hierarchical inheritance.
+ * Contexts are collection-scoped and inherit from parent directories.
+ * For example, context at "/talks" applies to "/talks/2024/keynote.md".
+ *
+ * @param db Database instance (unused - kept for compatibility)
+ * @param collectionName Collection name
+ * @param path Relative path within the collection
+ * @returns Context string or null if no context is defined
+ */
+export function getContextForPath(db, collectionName, path) {
+    const config = collectionsLoadConfig();
+    const coll = getCollection(collectionName);
+    if (!coll)
+        return null;
+    // Collect ALL matching contexts (global + all path prefixes)
+    const contexts = [];
+    // Add global context if present
+    if (config.global_context) {
+        contexts.push(config.global_context);
+    }
+    // Add all matching path contexts (from most general to most specific)
+    if (coll.context) {
+        const normalizedPath = path.startsWith("/") ? path : `/${path}`;
+        // Collect all matching prefixes
+        const matchingContexts = [];
+        for (const [prefix, context] of Object.entries(coll.context)) {
+            const normalizedPrefix = prefix.startsWith("/") ? prefix : `/${prefix}`;
+            if (normalizedPath.startsWith(normalizedPrefix)) {
+                matchingContexts.push({ prefix: normalizedPrefix, context });
+            }
+        }
+        // Sort by prefix length (shortest/most general first)
+        matchingContexts.sort((a, b) => a.prefix.length - b.prefix.length);
+        // Add all matching contexts
+        for (const match of matchingContexts) {
+            contexts.push(match.context);
+        }
+    }
+    // Join all contexts with double newline
+    return contexts.length > 0 ? contexts.join('\n\n') : null;
+}
+/**
+ * Get context for a file path (virtual or filesystem).
+ * Resolves the collection and relative path using the YAML collections config.
+ */
+export function getContextForFile(db, filepath) {
+    // Handle undefined or null filepath
+    if (!filepath)
+        return null;
+    // Get all collections from YAML config
+    const collections = collectionsListCollections();
+    const config = collectionsLoadConfig();
+    // Parse virtual path format: qmd://collection/path
+    let collectionName = null;
+    let relativePath = null;
+    const parsedVirtual = filepath.startsWith('qmd://') ? parseVirtualPath(filepath) : null;
+    if (parsedVirtual) {
+        collectionName = parsedVirtual.collectionName;
+        relativePath = parsedVirtual.path;
+    }
+    else {
+        // Filesystem path: find which collection this absolute path belongs to
+        for (const coll of collections) {
+            // Skip collections with missing paths
+            if (!coll || !coll.path)
+                continue;
+            if (filepath.startsWith(coll.path + '/') || filepath === coll.path) {
+                collectionName = coll.name;
+                // Extract relative path
+                relativePath = filepath.startsWith(coll.path + '/')
+                    ? filepath.slice(coll.path.length + 1)
+                    : '';
+                break;
+            }
+        }
+        if (!collectionName || relativePath === null)
+            return null;
+    }
+    // Get the collection from config
+    const coll = getCollection(collectionName);
+    if (!coll)
+        return null;
+    // Verify this document exists in the database
+    const doc = db.prepare(`
+    SELECT d.path
+    FROM documents d
+    WHERE d.collection = ? AND d.path = ? AND d.active = 1
+    LIMIT 1
+  `).get(collectionName, relativePath);
+    if (!doc)
+        return null;
+    // Collect ALL matching contexts (global + all path prefixes)
+    const contexts = [];
+    // Add global context if present
+    if (config.global_context) {
+        contexts.push(config.global_context);
+    }
+    // Add all matching path contexts (from most general to most specific)
+    if (coll.context) {
+        const normalizedPath = relativePath.startsWith("/") ? relativePath : `/${relativePath}`;
+        // Collect all matching prefixes
+        const matchingContexts = [];
+        for (const [prefix, context] of Object.entries(coll.context)) {
+            const normalizedPrefix = prefix.startsWith("/") ? prefix : `/${prefix}`;
+            if (normalizedPath.startsWith(normalizedPrefix)) {
+                matchingContexts.push({ prefix: normalizedPrefix, context });
+            }
+        }
+        // Sort by prefix length (shortest/most general first)
+        matchingContexts.sort((a, b) => a.prefix.length - b.prefix.length);
+        // Add all matching contexts
+        for (const match of matchingContexts) {
+            contexts.push(match.context);
+        }
+    }
+    // Join all contexts with double newline
+    return contexts.length > 0 ? contexts.join('\n\n') : null;
+}
+/**
+ * Get collection by name from YAML config.
+ * Returns collection metadata from ~/.config/qmd/index.yml
+ */
+export function getCollectionByName(db, name) {
+    const collection = getCollection(name);
+    if (!collection)
+        return null;
+    return {
+        name: collection.name,
+        pwd: collection.path,
+        glob_pattern: collection.pattern,
+    };
+}
+/**
+ * List all collections with document counts from database.
+ * Merges YAML config with database statistics.
+ */
+export function listCollections(db) {
+    const collections = collectionsListCollections();
+    // Get document counts from database for each collection
+    const result = collections.map(coll => {
+        const stats = db.prepare(`
+      SELECT
+        COUNT(d.id) as doc_count,
+        SUM(CASE WHEN d.active = 1 THEN 1 ELSE 0 END) as active_count,
+        MAX(d.modified_at) as last_modified
+      FROM documents d
+      WHERE d.collection = ?
+    `).get(coll.name);
+        return {
+            name: coll.name,
+            pwd: coll.path,
+            glob_pattern: coll.pattern,
+            doc_count: stats?.doc_count || 0,
+            active_count: stats?.active_count || 0,
+            last_modified: stats?.last_modified || null,
+        };
+    });
+    return result;
+}
+/**
+ * Remove a collection and clean up its documents.
+ * Uses collections.ts to remove from YAML config and cleans up database.
+ */
+export function removeCollection(db, collectionName) {
+    // Delete documents from database
+    const docResult = db.prepare(`DELETE FROM documents WHERE collection = ?`).run(collectionName);
+    // Clean up orphaned content hashes
+    const cleanupResult = db.prepare(`
+    DELETE FROM content
+    WHERE hash NOT IN (SELECT DISTINCT hash FROM documents WHERE active = 1)
+  `).run();
+    // Remove from YAML config (returns true if found and removed)
+    collectionsRemoveCollection(collectionName);
+    return {
+        deletedDocs: docResult.changes,
+        cleanedHashes: cleanupResult.changes
+    };
+}
+/**
+ * Rename a collection.
+ * Updates both YAML config and database documents table.
+ */
+export function renameCollection(db, oldName, newName) {
+    // Update all documents with the new collection name in database
+    db.prepare(`UPDATE documents SET collection = ? WHERE collection = ?`)
+        .run(newName, oldName);
+    // Rename in YAML config
+    collectionsRenameCollection(oldName, newName);
+}
+// =============================================================================
+// Context Management Operations
+// =============================================================================
+/**
+ * Insert or update a context for a specific collection and path prefix.
+ */
+export function insertContext(db, collectionId, pathPrefix, context) {
+    // Get collection name from ID
+    const coll = db.prepare(`SELECT name FROM collections WHERE id = ?`).get(collectionId);
+    if (!coll) {
+        throw new Error(`Collection with id ${collectionId} not found`);
+    }
+    // Use collections.ts to add context
+    collectionsAddContext(coll.name, pathPrefix, context);
+}
+/**
+ * Delete a context for a specific collection and path prefix.
+ * Returns the number of contexts deleted.
+ */
+export function deleteContext(db, collectionName, pathPrefix) {
+    // Use collections.ts to remove context
+    const success = collectionsRemoveContext(collectionName, pathPrefix);
+    return success ? 1 : 0;
+}
+/**
+ * Delete all global contexts (contexts with empty path_prefix).
+ * Returns the number of contexts deleted.
+ */
+export function deleteGlobalContexts(db) {
+    let deletedCount = 0;
+    // Remove global context
+    setGlobalContext(undefined);
+    deletedCount++;
+    // Remove root context (empty string) from all collections
+    const collections = collectionsListCollections();
+    for (const coll of collections) {
+        const success = collectionsRemoveContext(coll.name, '');
+        if (success) {
+            deletedCount++;
+        }
+    }
+    return deletedCount;
+}
+/**
+ * List all contexts, grouped by collection.
+ * Returns contexts ordered by collection name, then by path prefix length (longest first).
+ */
+export function listPathContexts(db) {
+    const allContexts = collectionsListAllContexts();
+    // Convert to expected format and sort
+    return allContexts.map(ctx => ({
+        collection_name: ctx.collection,
+        path_prefix: ctx.path,
+        context: ctx.context,
+    })).sort((a, b) => {
+        // Sort by collection name first
+        if (a.collection_name !== b.collection_name) {
+            return a.collection_name.localeCompare(b.collection_name);
+        }
+        // Then by path prefix length (longest first)
+        if (a.path_prefix.length !== b.path_prefix.length) {
+            return b.path_prefix.length - a.path_prefix.length;
+        }
+        // Then alphabetically
+        return a.path_prefix.localeCompare(b.path_prefix);
+    });
+}
+/**
+ * Get all collections (name only - from YAML config).
+ */
+export function getAllCollections(db) {
+    const collections = collectionsListCollections();
+    return collections.map(c => ({ name: c.name }));
+}
+/**
+ * Check which collections don't have any context defined.
+ * Returns collections that have no context entries at all (not even root context).
+ */
+export function getCollectionsWithoutContext(db) {
+    // Get all collections from YAML config
+    const yamlCollections = collectionsListCollections();
+    // Filter to those without context
+    const collectionsWithoutContext = [];
+    for (const coll of yamlCollections) {
+        // Check if collection has any context
+        if (!coll.context || Object.keys(coll.context).length === 0) {
+            // Get doc count from database
+            const stats = db.prepare(`
+        SELECT COUNT(d.id) as doc_count
+        FROM documents d
+        WHERE d.collection = ? AND d.active = 1
+      `).get(coll.name);
+            collectionsWithoutContext.push({
+                name: coll.name,
+                pwd: coll.path,
+                doc_count: stats?.doc_count || 0,
+            });
+        }
+    }
+    return collectionsWithoutContext.sort((a, b) => a.name.localeCompare(b.name));
+}
+/**
+ * Get top-level directories in a collection that don't have context.
+ * Useful for suggesting where context might be needed.
+ */
+export function getTopLevelPathsWithoutContext(db, collectionName) {
+    // Get all paths in the collection from database
+    const paths = db.prepare(`
+    SELECT DISTINCT path FROM documents
+    WHERE collection = ? AND active = 1
+  `).all(collectionName);
+    // Get existing contexts for this collection from YAML
+    const yamlColl = getCollection(collectionName);
+    if (!yamlColl)
+        return [];
+    const contextPrefixes = new Set();
+    if (yamlColl.context) {
+        for (const prefix of Object.keys(yamlColl.context)) {
+            contextPrefixes.add(prefix);
+        }
+    }
+    // Extract top-level directories (first path component)
+    const topLevelDirs = new Set();
+    for (const { path } of paths) {
+        const parts = path.split('/').filter(Boolean);
+        if (parts.length > 1) {
+            const dir = parts[0];
+            if (dir)
+                topLevelDirs.add(dir);
+        }
+    }
+    // Filter out directories that already have context (exact or parent)
+    const missing = [];
+    for (const dir of topLevelDirs) {
+        let hasContext = false;
+        // Check if this dir or any parent has context
+        for (const prefix of contextPrefixes) {
+            if (prefix === '' || prefix === dir || dir.startsWith(prefix + '/')) {
+                hasContext = true;
+                break;
+            }
+        }
+        if (!hasContext) {
+            missing.push(dir);
+        }
+    }
+    return missing.sort();
+}
+// =============================================================================
+// FTS Search
+// =============================================================================
+function sanitizeFTS5Term(term) {
+    return term.replace(/[^\p{L}\p{N}']/gu, '').toLowerCase();
+}
+function buildFTS5Query(query) {
+    const terms = query.split(/\s+/)
+        .map(t => sanitizeFTS5Term(t))
+        .filter(t => t.length > 0);
+    if (terms.length === 0)
+        return null;
+    if (terms.length === 1)
+        return `"${terms[0]}"*`;
+    return terms.map(t => `"${t}"*`).join(' AND ');
+}
+export function searchFTS(db, query, limit = 20, collectionName) {
+    const ftsQuery = buildFTS5Query(query);
+    if (!ftsQuery)
+        return [];
+    let sql = `
+    SELECT
+      'qmd://' || d.collection || '/' || d.path as filepath,
+      d.collection || '/' || d.path as display_path,
+      d.title,
+      content.doc as body,
+      d.hash,
+      bm25(documents_fts, 10.0, 1.0) as bm25_score
+    FROM documents_fts f
+    JOIN documents d ON d.id = f.rowid
+    JOIN content ON content.hash = d.hash
+    WHERE documents_fts MATCH ? AND d.active = 1
+  `;
+    const params = [ftsQuery];
+    if (collectionName) {
+        sql += ` AND d.collection = ?`;
+        params.push(String(collectionName));
+    }
+    // bm25 lower is better; sort ascending.
+    sql += ` ORDER BY bm25_score ASC LIMIT ?`;
+    params.push(limit);
+    const rows = db.prepare(sql).all(...params);
+    return rows.map(row => {
+        const collectionName = row.filepath.split('//')[1]?.split('/')[0] || "";
+        // Convert bm25 (negative, lower is better) into a stable [0..1) score where higher is better.
+        // FTS5 BM25 scores are negative (e.g., -10 is strong, -2 is weak).
+        // |x| / (1 + |x|) maps: strong(-10)→0.91, medium(-2)→0.67, weak(-0.5)→0.33, none(0)→0.
+        // Monotonic and query-independent — no per-query normalization needed.
+        const score = Math.abs(row.bm25_score) / (1 + Math.abs(row.bm25_score));
+        return {
+            filepath: row.filepath,
+            displayPath: row.display_path,
+            title: row.title,
+            hash: row.hash,
+            docid: getDocid(row.hash),
+            collectionName,
+            modifiedAt: "", // Not available in FTS query
+            bodyLength: row.body.length,
+            body: row.body,
+            context: getContextForFile(db, row.filepath),
+            score,
+            source: "fts",
+        };
+    });
+}
+// =============================================================================
+// Vector Search
+// =============================================================================
+export async function searchVec(db, query, model, limit = 20, collectionName, session, precomputedEmbedding) {
+    const tableExists = db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    if (!tableExists)
+        return [];
+    const embedding = precomputedEmbedding ?? await getEmbedding(query, model, true, session);
+    if (!embedding)
+        return [];
+    // IMPORTANT: We use a two-step query approach here because sqlite-vec virtual tables
+    // hang indefinitely when combined with JOINs in the same query. Do NOT try to
+    // "optimize" this by combining into a single query with JOINs - it will break.
+    // See: https://github.com/tobi/qmd/pull/23
+    // Step 1: Get vector matches from sqlite-vec (no JOINs allowed)
+    const vecResults = db.prepare(`
+    SELECT hash_seq, distance
+    FROM vectors_vec
+    WHERE embedding MATCH ? AND k = ?
+  `).all(new Float32Array(embedding), limit * 3);
+    if (vecResults.length === 0)
+        return [];
+    // Step 2: Get chunk info and document data
+    const hashSeqs = vecResults.map(r => r.hash_seq);
+    const distanceMap = new Map(vecResults.map(r => [r.hash_seq, r.distance]));
+    // Build query for document lookup
+    const placeholders = hashSeqs.map(() => '?').join(',');
+    let docSql = `
+    SELECT
+      cv.hash || '_' || cv.seq as hash_seq,
+      cv.hash,
+      cv.pos,
+      'qmd://' || d.collection || '/' || d.path as filepath,
+      d.collection || '/' || d.path as display_path,
+      d.title,
+      content.doc as body
+    FROM content_vectors cv
+    JOIN documents d ON d.hash = cv.hash AND d.active = 1
+    JOIN content ON content.hash = d.hash
+    WHERE cv.hash || '_' || cv.seq IN (${placeholders})
+  `;
+    const params = [...hashSeqs];
+    if (collectionName) {
+        docSql += ` AND d.collection = ?`;
+        params.push(collectionName);
+    }
+    const docRows = db.prepare(docSql).all(...params);
+    // Combine with distances and dedupe by filepath
+    const seen = new Map();
+    for (const row of docRows) {
+        const distance = distanceMap.get(row.hash_seq) ?? 1;
+        const existing = seen.get(row.filepath);
+        if (!existing || distance < existing.bestDist) {
+            seen.set(row.filepath, { row, bestDist: distance });
+        }
+    }
+    return Array.from(seen.values())
+        .sort((a, b) => a.bestDist - b.bestDist)
+        .slice(0, limit)
+        .map(({ row, bestDist }) => {
+        const collectionName = row.filepath.split('//')[1]?.split('/')[0] || "";
+        return {
+            filepath: row.filepath,
+            displayPath: row.display_path,
+            title: row.title,
+            hash: row.hash,
+            docid: getDocid(row.hash),
+            collectionName,
+            modifiedAt: "", // Not available in vec query
+            bodyLength: row.body.length,
+            body: row.body,
+            context: getContextForFile(db, row.filepath),
+            score: 1 - bestDist, // Cosine similarity = 1 - cosine distance
+            source: "vec",
+            chunkPos: row.pos,
+        };
+    });
+}
+// =============================================================================
+// Embeddings
+// =============================================================================
+async function getEmbedding(text, model, isQuery, session) {
+    // Format text using the appropriate prompt template
+    const formattedText = isQuery ? formatQueryForEmbedding(text) : formatDocForEmbedding(text);
+    const result = session
+        ? await session.embed(formattedText, { model, isQuery })
+        : await getDefaultLlamaCpp().embed(formattedText, { model, isQuery });
+    return result?.embedding || null;
+}
+/**
+ * Get all unique content hashes that need embeddings (from active documents).
+ * Returns hash, document body, and a sample path for display purposes.
+ */
+export function getHashesForEmbedding(db) {
+    return db.prepare(`
+    SELECT d.hash, c.doc as body, MIN(d.path) as path
+    FROM documents d
+    JOIN content c ON d.hash = c.hash
+    LEFT JOIN content_vectors v ON d.hash = v.hash AND v.seq = 0
+    WHERE d.active = 1 AND v.hash IS NULL
+    GROUP BY d.hash
+  `).all();
+}
+/**
+ * Clear all embeddings from the database (force re-index).
+ * Deletes all rows from content_vectors and drops the vectors_vec table.
+ */
+export function clearAllEmbeddings(db) {
+    db.exec(`DELETE FROM content_vectors`);
+    db.exec(`DROP TABLE IF EXISTS vectors_vec`);
+}
+/**
+ * Insert a single embedding into both content_vectors and vectors_vec tables.
+ * The hash_seq key is formatted as "hash_seq" for the vectors_vec table.
+ */
+export function insertEmbedding(db, hash, seq, pos, embedding, model, embeddedAt) {
+    const hashSeq = `${hash}_${seq}`;
+    const insertVecStmt = db.prepare(`INSERT OR REPLACE INTO vectors_vec (hash_seq, embedding) VALUES (?, ?)`);
+    const insertContentVectorStmt = db.prepare(`INSERT OR REPLACE INTO content_vectors (hash, seq, pos, model, embedded_at) VALUES (?, ?, ?, ?, ?)`);
+    insertVecStmt.run(hashSeq, embedding);
+    insertContentVectorStmt.run(hash, seq, pos, model, embeddedAt);
+}
+// =============================================================================
+// Query expansion
+// =============================================================================
+export async function expandQuery(query, model = DEFAULT_QUERY_MODEL, db) {
+    // Check cache first — stored as JSON preserving types
+    const cacheKey = getCacheKey("expandQuery", { query, model });
+    const cached = getCachedResult(db, cacheKey);
+    if (cached) {
+        try {
+            return JSON.parse(cached);
+        }
+        catch {
+            // Old cache format (pre-typed, newline-separated text) — re-expand
+        }
+    }
+    const llm = getDefaultLlamaCpp();
+    // Note: LlamaCpp uses hardcoded model, model parameter is ignored
+    const results = await llm.expandQuery(query);
+    // Map Queryable[] → ExpandedQuery[] (same shape, decoupled from llm.ts internals).
+    // Filter out entries that duplicate the original query text.
+    const expanded = results
+        .filter(r => r.text !== query)
+        .map(r => ({ type: r.type, text: r.text }));
+    if (expanded.length > 0) {
+        setCachedResult(db, cacheKey, JSON.stringify(expanded));
+    }
+    return expanded;
+}
+// =============================================================================
+// Reranking
+// =============================================================================
+export async function rerank(query, documents, model = DEFAULT_RERANK_MODEL, db) {
+    const cachedResults = new Map();
+    const uncachedDocs = [];
+    // Check cache for each document
+    // Cache key includes chunk text — different queries can select different chunks
+    // from the same file, and the reranker score depends on which chunk was sent.
+    for (const doc of documents) {
+        const cacheKey = getCacheKey("rerank", { query, file: doc.file, model, chunk: doc.text });
+        const cached = getCachedResult(db, cacheKey);
+        if (cached !== null) {
+            cachedResults.set(doc.file, parseFloat(cached));
+        }
+        else {
+            uncachedDocs.push({ file: doc.file, text: doc.text });
+        }
+    }
+    // Rerank uncached documents using LlamaCpp
+    if (uncachedDocs.length > 0) {
+        const llm = getDefaultLlamaCpp();
+        const rerankResult = await llm.rerank(query, uncachedDocs, { model });
+        // Cache results — use original doc.text for cache key (result.file lacks chunk text)
+        const textByFile = new Map(documents.map(d => [d.file, d.text]));
+        for (const result of rerankResult.results) {
+            const cacheKey = getCacheKey("rerank", { query, file: result.file, model, chunk: textByFile.get(result.file) || "" });
+            setCachedResult(db, cacheKey, result.score.toString());
+            cachedResults.set(result.file, result.score);
+        }
+    }
+    // Return all results sorted by score
+    return documents
+        .map(doc => ({ file: doc.file, score: cachedResults.get(doc.file) || 0 }))
+        .sort((a, b) => b.score - a.score);
+}
+// =============================================================================
+// Reciprocal Rank Fusion
+// =============================================================================
+export function reciprocalRankFusion(resultLists, weights = [], k = 60) {
+    const scores = new Map();
+    for (let listIdx = 0; listIdx < resultLists.length; listIdx++) {
+        const list = resultLists[listIdx];
+        if (!list)
+            continue;
+        const weight = weights[listIdx] ?? 1.0;
+        for (let rank = 0; rank < list.length; rank++) {
+            const result = list[rank];
+            if (!result)
+                continue;
+            const rrfContribution = weight / (k + rank + 1);
+            const existing = scores.get(result.file);
+            if (existing) {
+                existing.rrfScore += rrfContribution;
+                existing.topRank = Math.min(existing.topRank, rank);
+            }
+            else {
+                scores.set(result.file, {
+                    result,
+                    rrfScore: rrfContribution,
+                    topRank: rank,
+                });
+            }
+        }
+    }
+    // Top-rank bonus
+    for (const entry of scores.values()) {
+        if (entry.topRank === 0) {
+            entry.rrfScore += 0.05;
+        }
+        else if (entry.topRank <= 2) {
+            entry.rrfScore += 0.02;
+        }
+    }
+    return Array.from(scores.values())
+        .sort((a, b) => b.rrfScore - a.rrfScore)
+        .map(e => ({ ...e.result, score: e.rrfScore }));
+}
+/**
+ * Find a document by filename/path, docid (#hash), or with fuzzy matching.
+ * Returns document metadata without body by default.
+ *
+ * Supports:
+ * - Virtual paths: qmd://collection/path/to/file.md
+ * - Absolute paths: /path/to/file.md
+ * - Relative paths: path/to/file.md
+ * - Short docid: #abc123 (first 6 chars of hash)
+ */
+export function findDocument(db, filename, options = {}) {
+    let filepath = filename;
+    const colonMatch = filepath.match(/:(\d+)$/);
+    if (colonMatch) {
+        filepath = filepath.slice(0, -colonMatch[0].length);
+    }
+    // Check if this is a docid lookup (#abc123, abc123, "#abc123", "abc123", etc.)
+    if (isDocid(filepath)) {
+        const docidMatch = findDocumentByDocid(db, filepath);
+        if (docidMatch) {
+            filepath = docidMatch.filepath;
+        }
+        else {
+            return { error: "not_found", query: filename, similarFiles: [] };
+        }
+    }
+    if (filepath.startsWith('~/')) {
+        filepath = homedir() + filepath.slice(1);
+    }
+    const bodyCol = options.includeBody ? `, content.doc as body` : ``;
+    // Build computed columns
+    // Note: absoluteFilepath is computed from YAML collections after query
+    const selectCols = `
+    'qmd://' || d.collection || '/' || d.path as virtual_path,
+    d.collection || '/' || d.path as display_path,
+    d.title,
+    d.hash,
+    d.collection,
+    d.modified_at,
+    LENGTH(content.doc) as body_length
+    ${bodyCol}
+  `;
+    // Try to match by virtual path first
+    let doc = db.prepare(`
+    SELECT ${selectCols}
+    FROM documents d
+    JOIN content ON content.hash = d.hash
+    WHERE 'qmd://' || d.collection || '/' || d.path = ? AND d.active = 1
+  `).get(filepath);
+    // Try fuzzy match by virtual path
+    if (!doc) {
+        doc = db.prepare(`
+      SELECT ${selectCols}
+      FROM documents d
+      JOIN content ON content.hash = d.hash
+      WHERE 'qmd://' || d.collection || '/' || d.path LIKE ? AND d.active = 1
+      LIMIT 1
+    `).get(`%${filepath}`);
+    }
+    // Try to match by absolute path (requires looking up collection paths from YAML)
+    if (!doc && !filepath.startsWith('qmd://')) {
+        const collections = collectionsListCollections();
+        for (const coll of collections) {
+            let relativePath = null;
+            // If filepath is absolute and starts with collection path, extract relative part
+            if (filepath.startsWith(coll.path + '/')) {
+                relativePath = filepath.slice(coll.path.length + 1);
+            }
+            // Otherwise treat filepath as relative to collection
+            else if (!filepath.startsWith('/')) {
+                relativePath = filepath;
+            }
+            if (relativePath) {
+                doc = db.prepare(`
+          SELECT ${selectCols}
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE d.collection = ? AND d.path = ? AND d.active = 1
+        `).get(coll.name, relativePath);
+                if (doc)
+                    break;
+            }
+        }
+    }
+    if (!doc) {
+        const similar = findSimilarFiles(db, filepath, 5, 5);
+        return { error: "not_found", query: filename, similarFiles: similar };
+    }
+    // Get context using virtual path
+    const virtualPath = doc.virtual_path || `qmd://${doc.collection}/${doc.display_path}`;
+    const context = getContextForFile(db, virtualPath);
+    return {
+        filepath: virtualPath,
+        displayPath: doc.display_path,
+        title: doc.title,
+        context,
+        hash: doc.hash,
+        docid: getDocid(doc.hash),
+        collectionName: doc.collection,
+        modifiedAt: doc.modified_at,
+        bodyLength: doc.body_length,
+        ...(options.includeBody && doc.body !== undefined && { body: doc.body }),
+    };
+}
+/**
+ * Get the body content for a document
+ * Optionally slice by line range
+ */
+export function getDocumentBody(db, doc, fromLine, maxLines) {
+    const filepath = doc.filepath;
+    // Try to resolve document by filepath (absolute or virtual)
+    let row = null;
+    // Try virtual path first
+    if (filepath.startsWith('qmd://')) {
+        row = db.prepare(`
+      SELECT content.doc as body
+      FROM documents d
+      JOIN content ON content.hash = d.hash
+      WHERE 'qmd://' || d.collection || '/' || d.path = ? AND d.active = 1
+    `).get(filepath);
+    }
+    // Try absolute path by looking up in YAML collections
+    if (!row) {
+        const collections = collectionsListCollections();
+        for (const coll of collections) {
+            if (filepath.startsWith(coll.path + '/')) {
+                const relativePath = filepath.slice(coll.path.length + 1);
+                row = db.prepare(`
+          SELECT content.doc as body
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE d.collection = ? AND d.path = ? AND d.active = 1
+        `).get(coll.name, relativePath);
+                if (row)
+                    break;
+            }
+        }
+    }
+    if (!row)
+        return null;
+    let body = row.body;
+    if (fromLine !== undefined || maxLines !== undefined) {
+        const lines = body.split('\n');
+        const start = (fromLine || 1) - 1;
+        const end = maxLines !== undefined ? start + maxLines : lines.length;
+        body = lines.slice(start, end).join('\n');
+    }
+    return body;
+}
+/**
+ * Find multiple documents by glob pattern or comma-separated list
+ * Returns documents without body by default (use getDocumentBody to load)
+ */
+export function findDocuments(db, pattern, options = {}) {
+    const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?');
+    const errors = [];
+    const maxBytes = options.maxBytes ?? DEFAULT_MULTI_GET_MAX_BYTES;
+    const bodyCol = options.includeBody ? `, content.doc as body` : ``;
+    const selectCols = `
+    'qmd://' || d.collection || '/' || d.path as virtual_path,
+    d.collection || '/' || d.path as display_path,
+    d.title,
+    d.hash,
+    d.collection,
+    d.modified_at,
+    LENGTH(content.doc) as body_length
+    ${bodyCol}
+  `;
+    let fileRows;
+    if (isCommaSeparated) {
+        const names = pattern.split(',').map(s => s.trim()).filter(Boolean);
+        fileRows = [];
+        for (const name of names) {
+            let doc = db.prepare(`
+        SELECT ${selectCols}
+        FROM documents d
+        JOIN content ON content.hash = d.hash
+        WHERE 'qmd://' || d.collection || '/' || d.path = ? AND d.active = 1
+      `).get(name);
+            if (!doc) {
+                doc = db.prepare(`
+          SELECT ${selectCols}
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE 'qmd://' || d.collection || '/' || d.path LIKE ? AND d.active = 1
+          LIMIT 1
+        `).get(`%${name}`);
+            }
+            if (doc) {
+                fileRows.push(doc);
+            }
+            else {
+                const similar = findSimilarFiles(db, name, 5, 3);
+                let msg = `File not found: ${name}`;
+                if (similar.length > 0) {
+                    msg += ` (did you mean: ${similar.join(', ')}?)`;
+                }
+                errors.push(msg);
+            }
+        }
+    }
+    else {
+        // Glob pattern match
+        const matched = matchFilesByGlob(db, pattern);
+        if (matched.length === 0) {
+            errors.push(`No files matched pattern: ${pattern}`);
+            return { docs: [], errors };
+        }
+        const virtualPaths = matched.map(m => m.filepath);
+        const placeholders = virtualPaths.map(() => '?').join(',');
+        fileRows = db.prepare(`
+      SELECT ${selectCols}
+      FROM documents d
+      JOIN content ON content.hash = d.hash
+      WHERE 'qmd://' || d.collection || '/' || d.path IN (${placeholders}) AND d.active = 1
+    `).all(...virtualPaths);
+    }
+    const results = [];
+    for (const row of fileRows) {
+        // Get context using virtual path
+        const virtualPath = row.virtual_path || `qmd://${row.collection}/${row.display_path}`;
+        const context = getContextForFile(db, virtualPath);
+        if (row.body_length > maxBytes) {
+            results.push({
+                doc: { filepath: virtualPath, displayPath: row.display_path },
+                skipped: true,
+                skipReason: `File too large (${Math.round(row.body_length / 1024)}KB > ${Math.round(maxBytes / 1024)}KB)`,
+            });
+            continue;
+        }
+        results.push({
+            doc: {
+                filepath: virtualPath,
+                displayPath: row.display_path,
+                title: row.title || row.display_path.split('/').pop() || row.display_path,
+                context,
+                hash: row.hash,
+                docid: getDocid(row.hash),
+                collectionName: row.collection,
+                modifiedAt: row.modified_at,
+                bodyLength: row.body_length,
+                ...(options.includeBody && row.body !== undefined && { body: row.body }),
+            },
+            skipped: false,
+        });
+    }
+    return { docs: results, errors };
+}
+// =============================================================================
+// Status
+// =============================================================================
+export function getStatus(db) {
+    // Load collections from YAML
+    const yamlCollections = collectionsListCollections();
+    // Get document counts and last update times for each collection
+    const collections = yamlCollections.map(col => {
+        const stats = db.prepare(`
+      SELECT
+        COUNT(*) as active_count,
+        MAX(modified_at) as last_doc_update
+      FROM documents
+      WHERE collection = ? AND active = 1
+    `).get(col.name);
+        return {
+            name: col.name,
+            path: col.path,
+            pattern: col.pattern,
+            documents: stats.active_count,
+            lastUpdated: stats.last_doc_update || new Date().toISOString(),
+        };
+    });
+    // Sort by last update time (most recent first)
+    collections.sort((a, b) => {
+        if (!a.lastUpdated)
+            return 1;
+        if (!b.lastUpdated)
+            return -1;
+        return new Date(b.lastUpdated).getTime() - new Date(a.lastUpdated).getTime();
+    });
+    const totalDocs = db.prepare(`SELECT COUNT(*) as c FROM documents WHERE active = 1`).get().c;
+    const needsEmbedding = getHashesNeedingEmbedding(db);
+    const hasVectors = !!db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    return {
+        totalDocuments: totalDocs,
+        needsEmbedding,
+        hasVectorIndex: hasVectors,
+        collections,
+    };
+}
+export function extractSnippet(body, query, maxLen = 500, chunkPos, chunkLen) {
+    const totalLines = body.split('\n').length;
+    let searchBody = body;
+    let lineOffset = 0;
+    if (chunkPos && chunkPos > 0) {
+        // Search within the chunk region, with some padding for context
+        // Use provided chunkLen or fall back to max chunk size (covers variable-length chunks)
+        const searchLen = chunkLen || CHUNK_SIZE_CHARS;
+        const contextStart = Math.max(0, chunkPos - 100);
+        const contextEnd = Math.min(body.length, chunkPos + searchLen + 100);
+        searchBody = body.slice(contextStart, contextEnd);
+        if (contextStart > 0) {
+            lineOffset = body.slice(0, contextStart).split('\n').length - 1;
+        }
+    }
+    const lines = searchBody.split('\n');
+    const queryTerms = query.toLowerCase().split(/\s+/).filter(t => t.length > 0);
+    let bestLine = 0, bestScore = -1;
+    for (let i = 0; i < lines.length; i++) {
+        const lineLower = (lines[i] ?? "").toLowerCase();
+        let score = 0;
+        for (const term of queryTerms) {
+            if (lineLower.includes(term))
+                score++;
+        }
+        if (score > bestScore) {
+            bestScore = score;
+            bestLine = i;
+        }
+    }
+    const start = Math.max(0, bestLine - 1);
+    const end = Math.min(lines.length, bestLine + 3);
+    const snippetLines = lines.slice(start, end);
+    let snippetText = snippetLines.join('\n');
+    // If we focused on a chunk window and it produced an empty/whitespace-only snippet,
+    // fall back to a full-document snippet so we always show something useful.
+    if (chunkPos && chunkPos > 0 && snippetText.trim().length === 0) {
+        return extractSnippet(body, query, maxLen, undefined);
+    }
+    if (snippetText.length > maxLen)
+        snippetText = snippetText.substring(0, maxLen - 3) + "...";
+    const absoluteStart = lineOffset + start + 1; // 1-indexed
+    const snippetLineCount = snippetLines.length;
+    const linesBefore = absoluteStart - 1;
+    const linesAfter = totalLines - (absoluteStart + snippetLineCount - 1);
+    // Format with diff-style header: @@ -start,count @@ (linesBefore before, linesAfter after)
+    const header = `@@ -${absoluteStart},${snippetLineCount} @@ (${linesBefore} before, ${linesAfter} after)`;
+    const snippet = `${header}\n${snippetText}`;
+    return {
+        line: lineOffset + bestLine + 1,
+        snippet,
+        linesBefore,
+        linesAfter,
+        snippetLines: snippetLineCount,
+    };
+}
+// =============================================================================
+// Shared helpers (used by both CLI and MCP)
+// =============================================================================
+/**
+ * Add line numbers to text content.
+ * Each line becomes: "{lineNum}: {content}"
+ */
+export function addLineNumbers(text, startLine = 1) {
+    const lines = text.split('\n');
+    return lines.map((line, i) => `${startLine + i}: ${line}`).join('\n');
+}
+/**
+ * Hybrid search: BM25 + vector + query expansion + RRF + chunked reranking.
+ *
+ * Pipeline:
+ * 1. BM25 probe → skip expansion if strong signal
+ * 2. expandQuery() → typed query variants (lex/vec/hyde)
+ * 3. Type-routed search: original→vector, lex→FTS, vec/hyde→vector
+ * 4. RRF fusion → slice to candidateLimit
+ * 5. chunkDocument() + keyword-best-chunk selection
+ * 6. rerank on chunks (NOT full bodies — O(tokens) trap)
+ * 7. Position-aware score blending (RRF rank × reranker score)
+ * 8. Dedup by file, filter by minScore, slice to limit
+ */
+export async function hybridQuery(store, query, options) {
+    const limit = options?.limit ?? 10;
+    const minScore = options?.minScore ?? 0;
+    const candidateLimit = options?.candidateLimit ?? RERANK_CANDIDATE_LIMIT;
+    const collection = options?.collection;
+    const hooks = options?.hooks;
+    const rankedLists = [];
+    const docidMap = new Map(); // filepath -> docid
+    const hasVectors = !!store.db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    // Step 1: BM25 probe — strong signal skips expensive LLM expansion
+    // Pass collection directly into FTS query (filter at SQL level, not post-hoc)
+    const initialFts = store.searchFTS(query, 20, collection);
+    const topScore = initialFts[0]?.score ?? 0;
+    const secondScore = initialFts[1]?.score ?? 0;
+    const hasStrongSignal = initialFts.length > 0
+        && topScore >= STRONG_SIGNAL_MIN_SCORE
+        && (topScore - secondScore) >= STRONG_SIGNAL_MIN_GAP;
+    if (hasStrongSignal)
+        hooks?.onStrongSignal?.(topScore);
+    // Step 2: Expand query (or skip if strong signal)
+    const expanded = hasStrongSignal
+        ? []
+        : await store.expandQuery(query);
+    hooks?.onExpand?.(query, expanded);
+    // Seed with initial FTS results (avoid re-running original query FTS)
+    if (initialFts.length > 0) {
+        for (const r of initialFts)
+            docidMap.set(r.filepath, r.docid);
+        rankedLists.push(initialFts.map(r => ({
+            file: r.filepath, displayPath: r.displayPath,
+            title: r.title, body: r.body || "", score: r.score,
+        })));
+    }
+    // Step 3: Route searches by query type
+    //
+    // Strategy: run all FTS queries immediately (they're sync/instant), then
+    // batch-embed all vector queries in one embedBatch() call, then run
+    // sqlite-vec lookups with pre-computed embeddings.
+    // 3a: Run FTS for all lex expansions right away (no LLM needed)
+    for (const q of expanded) {
+        if (q.type === 'lex') {
+            const ftsResults = store.searchFTS(q.text, 20, collection);
+            if (ftsResults.length > 0) {
+                for (const r of ftsResults)
+                    docidMap.set(r.filepath, r.docid);
+                rankedLists.push(ftsResults.map(r => ({
+                    file: r.filepath, displayPath: r.displayPath,
+                    title: r.title, body: r.body || "", score: r.score,
+                })));
+            }
+        }
+    }
+    // 3b: Collect all texts that need vector search (original query + vec/hyde expansions)
+    if (hasVectors) {
+        const vecQueries = [
+            { text: query, isOriginal: true },
+        ];
+        for (const q of expanded) {
+            if (q.type === 'vec' || q.type === 'hyde') {
+                vecQueries.push({ text: q.text, isOriginal: false });
+            }
+        }
+        // Batch embed all vector queries in a single call
+        const llm = getDefaultLlamaCpp();
+        const textsToEmbed = vecQueries.map(q => formatQueryForEmbedding(q.text));
+        const embeddings = await llm.embedBatch(textsToEmbed);
+        // Run sqlite-vec lookups with pre-computed embeddings
+        for (let i = 0; i < vecQueries.length; i++) {
+            const embedding = embeddings[i]?.embedding;
+            if (!embedding)
+                continue;
+            const vecResults = await store.searchVec(vecQueries[i].text, DEFAULT_EMBED_MODEL, 20, collection, undefined, embedding);
+            if (vecResults.length > 0) {
+                for (const r of vecResults)
+                    docidMap.set(r.filepath, r.docid);
+                rankedLists.push(vecResults.map(r => ({
+                    file: r.filepath, displayPath: r.displayPath,
+                    title: r.title, body: r.body || "", score: r.score,
+                })));
+            }
+        }
+    }
+    // Step 4: RRF fusion — first 2 lists (original FTS + first vec) get 2x weight
+    const weights = rankedLists.map((_, i) => i < 2 ? 2.0 : 1.0);
+    const fused = reciprocalRankFusion(rankedLists, weights);
+    const candidates = fused.slice(0, candidateLimit);
+    if (candidates.length === 0)
+        return [];
+    // Step 5: Chunk documents, pick best chunk per doc for reranking.
+    // Reranking full bodies is O(tokens) — the critical perf lesson that motivated this refactor.
+    const queryTerms = query.toLowerCase().split(/\s+/).filter(t => t.length > 2);
+    const chunksToRerank = [];
+    const docChunkMap = new Map();
+    for (const cand of candidates) {
+        const chunks = chunkDocument(cand.body);
+        if (chunks.length === 0)
+            continue;
+        // Pick chunk with most keyword overlap (fallback: first chunk)
+        let bestIdx = 0;
+        let bestScore = -1;
+        for (let i = 0; i < chunks.length; i++) {
+            const chunkLower = chunks[i].text.toLowerCase();
+            const score = queryTerms.reduce((acc, term) => acc + (chunkLower.includes(term) ? 1 : 0), 0);
+            if (score > bestScore) {
+                bestScore = score;
+                bestIdx = i;
+            }
+        }
+        chunksToRerank.push({ file: cand.file, text: chunks[bestIdx].text });
+        docChunkMap.set(cand.file, { chunks, bestIdx });
+    }
+    // Step 6: Rerank chunks (NOT full bodies)
+    hooks?.onRerankStart?.(chunksToRerank.length);
+    const reranked = await store.rerank(query, chunksToRerank);
+    hooks?.onRerankDone?.();
+    // Step 7: Blend RRF position score with reranker score
+    // Position-aware weights: top retrieval results get more protection from reranker disagreement
+    const candidateMap = new Map(candidates.map(c => [c.file, {
+            displayPath: c.displayPath, title: c.title, body: c.body,
+        }]));
+    const rrfRankMap = new Map(candidates.map((c, i) => [c.file, i + 1]));
+    const blended = reranked.map(r => {
+        const rrfRank = rrfRankMap.get(r.file) || candidateLimit;
+        let rrfWeight;
+        if (rrfRank <= 3)
+            rrfWeight = 0.75;
+        else if (rrfRank <= 10)
+            rrfWeight = 0.60;
+        else
+            rrfWeight = 0.40;
+        const rrfScore = 1 / rrfRank;
+        const blendedScore = rrfWeight * rrfScore + (1 - rrfWeight) * r.score;
+        const candidate = candidateMap.get(r.file);
+        const chunkInfo = docChunkMap.get(r.file);
+        const bestIdx = chunkInfo?.bestIdx ?? 0;
+        const bestChunk = chunkInfo?.chunks[bestIdx]?.text || candidate?.body || "";
+        const bestChunkPos = chunkInfo?.chunks[bestIdx]?.pos || 0;
+        return {
+            file: r.file,
+            displayPath: candidate?.displayPath || "",
+            title: candidate?.title || "",
+            body: candidate?.body || "",
+            bestChunk,
+            bestChunkPos,
+            score: blendedScore,
+            context: store.getContextForFile(r.file),
+            docid: docidMap.get(r.file) || "",
+        };
+    }).sort((a, b) => b.score - a.score);
+    // Step 8: Dedup by file (safety net — prevents duplicate output)
+    const seenFiles = new Set();
+    return blended
+        .filter(r => {
+        if (seenFiles.has(r.file))
+            return false;
+        seenFiles.add(r.file);
+        return true;
+    })
+        .filter(r => r.score >= minScore)
+        .slice(0, limit);
+}
+/**
+ * Vector-only semantic search with query expansion.
+ *
+ * Pipeline:
+ * 1. expandQuery() → typed variants, filter to vec/hyde only (lex irrelevant here)
+ * 2. searchVec() for original + vec/hyde variants (sequential — node-llama-cpp embed limitation)
+ * 3. Dedup by filepath (keep max score)
+ * 4. Sort by score descending, filter by minScore, slice to limit
+ */
+export async function vectorSearchQuery(store, query, options) {
+    const limit = options?.limit ?? 10;
+    const minScore = options?.minScore ?? 0.3;
+    const collection = options?.collection;
+    const hasVectors = !!store.db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    if (!hasVectors)
+        return [];
+    // Expand query — filter to vec/hyde only (lex queries target FTS, not vector)
+    const allExpanded = await store.expandQuery(query);
+    const vecExpanded = allExpanded.filter(q => q.type !== 'lex');
+    options?.hooks?.onExpand?.(query, vecExpanded);
+    // Run original + vec/hyde expanded through vector, sequentially — concurrent embed() hangs
+    const queryTexts = [query, ...vecExpanded.map(q => q.text)];
+    const allResults = new Map();
+    for (const q of queryTexts) {
+        const vecResults = await store.searchVec(q, DEFAULT_EMBED_MODEL, limit, collection);
+        for (const r of vecResults) {
+            const existing = allResults.get(r.filepath);
+            if (!existing || r.score > existing.score) {
+                allResults.set(r.filepath, {
+                    file: r.filepath,
+                    displayPath: r.displayPath,
+                    title: r.title,
+                    body: r.body || "",
+                    score: r.score,
+                    context: store.getContextForFile(r.filepath),
+                    docid: r.docid,
+                });
+            }
+        }
+    }
+    return Array.from(allResults.values())
+        .sort((a, b) => b.score - a.score)
+        .filter(r => r.score >= minScore)
+        .slice(0, limit);
+}