@joycodetech/qmd-ja 2.5.3-ja.3

package/dist/cli/qmd.js

@@ -0,0 +1,4179 @@
+import { isBun, openDatabase } from "../db.js";
+import fastGlob from "fast-glob";
+import { execSync, spawn as nodeSpawn } from "child_process";
+import { fileURLToPath } from "url";
+import { basename, dirname, join as pathJoin, relative as relativePath, resolve as pathResolve } from "path";
+import { parseArgs } from "util";
+import { readFileSync, readdirSync, realpathSync, statSync, existsSync, unlinkSync, writeFileSync, openSync, closeSync, mkdirSync, lstatSync, rmSync, symlinkSync, readlinkSync, copyFileSync } from "fs";
+import { createInterface } from "readline/promises";
+import { getPwd, getRealPath, homedir, resolve, enableProductionMode, searchFTS, extractSnippet, getContextForFile, getContextForPath, listCollections, removeCollection, renameCollection, findSimilarFiles, findDocumentByDocid, isDocid, matchFilesByGlob, getHashesNeedingEmbedding, clearAllEmbeddings, insertEmbedding, getStatus, hashContent, extractTitle, formatDocForEmbedding, getEmbeddingFingerprint, chunkDocumentByTokens, clearCache, getCacheKey, getCachedResult, setCachedResult, getIndexHealth, parseVirtualPath, buildVirtualPath, isVirtualPath, resolveVirtualPath, toVirtualPath, insertContent, insertDocument, findActiveDocument, findOrMigrateLegacyDocument, updateDocumentTitle, updateDocument, deactivateDocument, getActiveDocumentPaths, cleanupOrphanedContent, deleteLLMCache, deleteInactiveDocuments, cleanupOrphanedVectors, vacuumDatabase, getCollectionsWithoutContext, getTopLevelPathsWithoutContext, handelize, hybridQuery, vectorSearchQuery, structuredSearch, addLineNumbers, DEFAULT_EMBED_MODEL, DEFAULT_EMBED_MAX_BATCH_BYTES, DEFAULT_EMBED_MAX_DOCS_PER_BATCH, DEFAULT_RERANK_MODEL, DEFAULT_QUERY_MODEL, DEFAULT_GLOB, DEFAULT_MULTI_GET_MAX_BYTES, createStore, getDefaultDbPath, reindexCollection, initializeKuromojiTokenizer, initializeVaporettoTokenizer, FTS_CJK_NORMALIZED_VERSION, resolveVaporettoModelPath, generateEmbeddings, maybeAdoptLegacyEmbeddingFingerprint, syncConfigToDb, } from "../store.js";
+import { disposeDefaultLlamaCpp, getDefaultLlamaCpp, setDefaultLlamaCpp, LlamaCpp, withLLMSession, pullModels, DEFAULT_MODEL_CACHE_DIR, resolveEmbedModel, resolveGenerateModel, resolveRerankModel, resolveModels, inspectGgufFile, isDarwinMetalMitigationActive } from "../llm.js";
+import { formatSearchResults, formatDocuments, escapeXml, escapeCSV, } from "./formatter.js";
+import { getCollection as getCollectionFromYaml, listCollections as yamlListCollections, getDefaultCollectionNames, addContext as yamlAddContext, removeContext as yamlRemoveContext, removeCollection as yamlRemoveCollectionFn, renameCollection as yamlRenameCollectionFn, setGlobalContext, listAllContexts, setConfigIndexName, loadConfig, saveConfig, setConfigSource, findLocalConfigPath, getLocalDbPath, getConfigPath, configExists, } from "../collections.js";
+// NOTE: enableProductionMode() is intentionally NOT called at module scope here.
+// Importing this module for its exports (e.g. buildEditorUri, termLink from
+// test/cli.test.ts) must not flip the global production flag, as that leaks
+// into unrelated tests that rely on the default (development) database path
+// resolution. The flag is flipped inside the CLI's main-module guard below so
+// it only fires when qmd is actually invoked as a script.
+// =============================================================================
+// Store/DB lifecycle (no legacy singletons in store.ts)
+// =============================================================================
+let store = null;
+let storeDbPathOverride;
+let currentIndexName = "index";
+function getStore() {
+    if (!store) {
+        store = createStore(storeDbPathOverride);
+        // Sync YAML config into SQLite store_collections so store.ts reads from DB
+        try {
+            const activeModels = ensureModelsConfiguredForCli();
+            const config = loadConfig();
+            syncConfigToDb(store.db, config);
+            setDefaultLlamaCpp(new LlamaCpp({
+                embedModel: activeModels.embed,
+                generateModel: activeModels.generate,
+                rerankModel: activeModels.rerank,
+            }));
+        }
+        catch {
+            // Config may not exist yet — that's fine, DB works without it
+        }
+    }
+    return store;
+}
+function getDb() {
+    return getStore().db;
+}
+/** Re-sync YAML config into SQLite after CLI mutations (add/remove/rename collection, context changes) */
+function resyncConfig() {
+    const s = getStore();
+    try {
+        const config = loadConfig();
+        // Clear config hash to force re-sync
+        s.db.prepare(`DELETE FROM store_config WHERE key = 'config_hash'`).run();
+        syncConfigToDb(s.db, config);
+    }
+    catch {
+        // Config may not exist — that's fine
+    }
+}
+function closeDb() {
+    if (store) {
+        store.close();
+        store = null;
+    }
+}
+function getDbPath() {
+    return store?.dbPath ?? storeDbPathOverride ?? getDefaultDbPath();
+}
+function getActiveIndexName() {
+    return currentIndexName;
+}
+function setIndexName(name) {
+    let normalizedName = name;
+    // Normalize relative paths to prevent malformed database paths
+    if (name && name.includes('/')) {
+        const absolutePath = pathResolve(process.cwd(), name);
+        // Replace path separators with underscores to create a valid filename
+        normalizedName = absolutePath.replace(/\//g, '_').replace(/^_/, '');
+    }
+    currentIndexName = normalizedName || "index";
+    storeDbPathOverride = normalizedName ? getDefaultDbPath(normalizedName) : undefined;
+    // Reset open handle so next use opens the new index
+    closeDb();
+}
+function ensureVecTable(_db, dimensions) {
+    // Store owns the DB; ignore `_db` and ensure vec table on the active store
+    getStore().ensureVecTable(dimensions);
+}
+// Terminal colors (respects NO_COLOR env)
+const useColor = !process.env.NO_COLOR && process.stdout.isTTY;
+const c = {
+    reset: useColor ? "\x1b[0m" : "",
+    dim: useColor ? "\x1b[2m" : "",
+    bold: useColor ? "\x1b[1m" : "",
+    cyan: useColor ? "\x1b[36m" : "",
+    yellow: useColor ? "\x1b[33m" : "",
+    green: useColor ? "\x1b[32m" : "",
+    magenta: useColor ? "\x1b[35m" : "",
+    blue: useColor ? "\x1b[34m" : "",
+};
+// Terminal cursor control
+const cursor = {
+    hide() { process.stderr.write('\x1b[?25l'); },
+    show() { process.stderr.write('\x1b[?25h'); },
+};
+async function flushWritable(stream) {
+    await new Promise((resolve) => {
+        stream.write("", () => resolve());
+    });
+}
+/**
+ * Finish a successful CLI command after output has been flushed.
+ *
+ * We deliberately do NOT call `process.exit(0)`. `process.exit()` skips
+ * Node's `beforeExit` event, and node-llama-cpp registers a `beforeExit` hook
+ * that auto-disposes its native handles. On darwin, without that hook firing,
+ * libggml-metal's static `ggml_metal_device` destructor asserts on a
+ * non-empty residency-set collection during `__cxa_finalize_ranges` and
+ * dumps a multi-kB backtrace (upstream ggml-org/llama.cpp#22593, fix open as
+ * PR #22595). Empirically, even with explicit `disposeDefaultLlamaCpp()` the
+ * direct `process.exit(0)` path still trips the assertion — letting the
+ * event loop drain naturally is what actually clears the rsets.
+ *
+ * So: set `process.exitCode = 0` and return. The main module finishes, the
+ * event loop drains, `beforeExit` fires, native resources tear down in
+ * order, and the process exits cleanly. The `GGML_METAL_NO_RESIDENCY=1` env
+ * var that `bin/qmd` exports is a defense-in-depth safety net for paths
+ * that still call `process.exit()` after loading the native binding
+ * (signal handlers, error paths, `bun test`).
+ *
+ * If the caller passes an explicit `exit` for testability, we honor it —
+ * the lifecycle tests verify the legacy flush → cleanup → exit ordering.
+ * Production callers must not pass `exit`.
+ */
+export async function finishSuccessfulCliCommand(options) {
+    const stderr = options.stderr ?? process.stderr;
+    await flushWritable(options.stdout ?? process.stdout);
+    try {
+        await (options.cleanup ?? disposeDefaultLlamaCpp)();
+    }
+    catch (error) {
+        stderr.write(`QMD Warning: cleanup after successful output failed (${error instanceof Error ? error.message : String(error)}); exiting 0 because command output completed.\n`);
+    }
+    await flushWritable(stderr);
+    if (options.exit) {
+        options.exit(0);
+        return;
+    }
+    process.exitCode = 0;
+}
+// Ensure cursor is restored on exit
+process.on('SIGINT', () => { cursor.show(); process.exit(130); });
+process.on('SIGTERM', () => { cursor.show(); process.exit(143); });
+// Terminal progress bar using OSC 9;4 escape sequence (TTY only)
+const isTTY = process.stderr.isTTY;
+const progress = {
+    set(percent) {
+        if (isTTY)
+            process.stderr.write(`\x1b]9;4;1;${Math.round(percent)}\x07`);
+    },
+    clear() {
+        if (isTTY)
+            process.stderr.write(`\x1b]9;4;0\x07`);
+    },
+    indeterminate() {
+        if (isTTY)
+            process.stderr.write(`\x1b]9;4;3\x07`);
+    },
+    error() {
+        if (isTTY)
+            process.stderr.write(`\x1b]9;4;2\x07`);
+    },
+};
+// Format seconds into human-readable ETA
+function formatETA(seconds) {
+    if (seconds < 60)
+        return `${Math.round(seconds)}s`;
+    if (seconds < 3600)
+        return `${Math.floor(seconds / 60)}m ${Math.round(seconds % 60)}s`;
+    return `${Math.floor(seconds / 3600)}h ${Math.floor((seconds % 3600) / 60)}m`;
+}
+// Check index health and print warnings/tips
+function checkIndexHealth(db, model = resolveEmbedModelForCli()) {
+    const { needsEmbedding, totalDocs, daysStale } = getIndexHealth(db, model);
+    // Warn if many docs need embedding
+    if (needsEmbedding > 0) {
+        const pct = Math.round((needsEmbedding / totalDocs) * 100);
+        if (pct >= 10) {
+            process.stderr.write(`${c.yellow}Warning: ${needsEmbedding} documents (${pct}%) need embeddings. Run 'qmd embed' for better results.${c.reset}\n`);
+        }
+        else {
+            process.stderr.write(`${c.dim}Tip: ${needsEmbedding} documents need embeddings. Run 'qmd embed' to index them.${c.reset}\n`);
+        }
+    }
+    // Check if most recent document update is older than 2 weeks
+    if (daysStale !== null && daysStale >= 14) {
+        process.stderr.write(`${c.dim}Tip: Index last updated ${daysStale} days ago. Run 'qmd update' to refresh.${c.reset}\n`);
+    }
+}
+// Compute unique display path for a document
+// Always include at least parent folder + filename, add more parent dirs until unique
+function computeDisplayPath(filepath, collectionPath, existingPaths) {
+    // Get path relative to collection (include collection dir name)
+    const collectionDir = collectionPath.replace(/\/$/, '');
+    const collectionName = collectionDir.split('/').pop() || '';
+    let relativePath;
+    if (filepath.startsWith(collectionDir + '/')) {
+        // filepath is under collection: use collection name + relative path
+        relativePath = collectionName + filepath.slice(collectionDir.length);
+    }
+    else {
+        // Fallback: just use the filepath
+        relativePath = filepath;
+    }
+    const parts = relativePath.split('/').filter(p => p.length > 0);
+    // Always include at least parent folder + filename (minimum 2 parts if available)
+    // Then add more parent dirs until unique
+    const minParts = Math.min(2, parts.length);
+    for (let i = parts.length - minParts; i >= 0; i--) {
+        const candidate = parts.slice(i).join('/');
+        if (!existingPaths.has(candidate)) {
+            return candidate;
+        }
+    }
+    // Absolute fallback: use full path (should be unique)
+    return filepath;
+}
+function formatTimeAgo(date) {
+    const seconds = Math.floor((Date.now() - date.getTime()) / 1000);
+    if (seconds < 60)
+        return `${seconds}s ago`;
+    const minutes = Math.floor(seconds / 60);
+    if (minutes < 60)
+        return `${minutes}m ago`;
+    const hours = Math.floor(minutes / 60);
+    if (hours < 24)
+        return `${hours}h ago`;
+    const days = Math.floor(hours / 24);
+    return `${days}d ago`;
+}
+function formatMs(ms) {
+    if (ms < 1000)
+        return `${ms}ms`;
+    return `${(ms / 1000).toFixed(1)}s`;
+}
+function formatBytes(bytes) {
+    if (bytes < 1024)
+        return `${bytes} B`;
+    if (bytes < 1024 * 1024)
+        return `${(bytes / 1024).toFixed(1)} KB`;
+    if (bytes < 1024 * 1024 * 1024)
+        return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
+    return `${(bytes / (1024 * 1024 * 1024)).toFixed(1)} GB`;
+}
+function sameDirectory(a, b) {
+    try {
+        return realpathSync(a) === realpathSync(b);
+    }
+    catch {
+        return pathResolve(a) === pathResolve(b);
+    }
+}
+function initLocalIndex() {
+    const cwd = getPwd();
+    if (sameDirectory(cwd, homedir())) {
+        throw new Error("Refusing to initialize a local index in $HOME. The global index is automatically created; run `qmd collection add <path>` for the global index, or run `qmd init` inside a project folder.");
+    }
+    const qmdDir = pathJoin(cwd, ".qmd");
+    const ymlPath = pathJoin(qmdDir, "index.yml");
+    const yamlPath = pathJoin(qmdDir, "index.yaml");
+    const configPath = existsSync(yamlPath) ? yamlPath : ymlPath;
+    const dbPath = pathJoin(qmdDir, "index.sqlite");
+    mkdirSync(qmdDir, { recursive: true });
+    setConfigSource({ configPath });
+    storeDbPathOverride = dbPath;
+    closeDb();
+    if (!existsSync(configPath)) {
+        saveConfig({
+            collections: {},
+            models: resolveModels(),
+        });
+    }
+    else {
+        ensureModelsConfiguredForCli();
+    }
+    const localStore = createStore(dbPath);
+    syncConfigToDb(localStore.db, loadConfig());
+    localStore.close();
+    console.log("ready to go with new local index");
+}
+function isForceCpuEnabled() {
+    const value = process.env.QMD_FORCE_CPU;
+    return !!value && !["false", "off", "none", "disable", "disabled", "0"].includes(value.trim().toLowerCase());
+}
+function configuredGpuModeLabel() {
+    return isForceCpuEnabled()
+        ? "CPU forced (QMD_FORCE_CPU)"
+        : (process.env.QMD_LLAMA_GPU?.trim() || "auto");
+}
+function summarizeDeviceNames(names) {
+    const counts = new Map();
+    for (const name of names) {
+        counts.set(name, (counts.get(name) || 0) + 1);
+    }
+    return Array.from(counts.entries())
+        .map(([name, count]) => count > 1 ? `${count}× ${name}` : name)
+        .join(", ");
+}
+function sanitizeDiagnosticMessage(message) {
+    const home = homedir();
+    return message
+        .replaceAll(home, "~")
+        .replaceAll(process.cwd(), ".")
+        .split("\n")
+        .map(line => line.trim())
+        .filter(Boolean)
+        .slice(0, 3)
+        .join("; ");
+}
+async function showStatus() {
+    const dbPath = getDbPath();
+    const db = getDb();
+    // Collections are defined in YAML; no duplicate cleanup needed.
+    // Collections are defined in YAML; no duplicate cleanup needed.
+    // Index size
+    let indexSize = 0;
+    try {
+        const stat = statSync(dbPath).size;
+        indexSize = stat;
+    }
+    catch { }
+    // Collections info (from YAML + database stats)
+    const collections = listCollections(db);
+    // Overall stats
+    const totalDocs = db.prepare(`SELECT COUNT(*) as count FROM documents WHERE active = 1`).get();
+    const vectorCount = db.prepare(`SELECT COUNT(*) as count FROM content_vectors`).get();
+    const statusEmbedModel = resolveEmbedModelForCli();
+    const needsEmbedding = getHashesNeedingEmbedding(db, undefined, statusEmbedModel);
+    // Most recent update across all collections
+    const mostRecent = db.prepare(`SELECT MAX(modified_at) as latest FROM documents WHERE active = 1`).get();
+    console.log(`${c.bold}QMD Status${c.reset}\n`);
+    console.log(`Index: ${dbPath}`);
+    console.log(`Size:  ${formatBytes(indexSize)}`);
+    // MCP daemon status (check PID file liveness)
+    const mcpCacheDir = process.env.XDG_CACHE_HOME
+        ? resolve(process.env.XDG_CACHE_HOME, "qmd")
+        : resolve(homedir(), ".cache", "qmd");
+    const mcpPidPath = resolve(mcpCacheDir, "mcp.pid");
+    if (existsSync(mcpPidPath)) {
+        const mcpPid = parseInt(readFileSync(mcpPidPath, "utf-8").trim());
+        try {
+            process.kill(mcpPid, 0);
+            console.log(`MCP:   ${c.green}running${c.reset} (PID ${mcpPid})`);
+        }
+        catch {
+            unlinkSync(mcpPidPath);
+            // Stale PID file cleaned up silently
+        }
+    }
+    console.log("");
+    console.log(`${c.bold}Documents${c.reset}`);
+    console.log(`  Total:    ${totalDocs.count} files indexed`);
+    console.log(`  Vectors:  ${vectorCount.count} embedded`);
+    if (needsEmbedding > 0) {
+        console.log(`  ${c.yellow}Pending:  ${needsEmbedding} need embedding${c.reset} (run 'qmd embed')`);
+    }
+    if (mostRecent.latest) {
+        const lastUpdate = new Date(mostRecent.latest);
+        console.log(`  Updated:  ${formatTimeAgo(lastUpdate)}`);
+    }
+    // Get all contexts grouped by collection (from YAML)
+    const allContexts = listAllContexts();
+    const contextsByCollection = new Map();
+    for (const ctx of allContexts) {
+        // Group contexts by collection name
+        if (!contextsByCollection.has(ctx.collection)) {
+            contextsByCollection.set(ctx.collection, []);
+        }
+        contextsByCollection.get(ctx.collection).push({
+            path_prefix: ctx.path,
+            context: ctx.context
+        });
+    }
+    // AST chunking status
+    try {
+        const { getASTStatus } = await import("../ast.js");
+        const ast = await getASTStatus();
+        console.log(`\n${c.bold}AST Chunking${c.reset}`);
+        if (ast.available) {
+            const ok = ast.languages.filter(l => l.available).map(l => l.language);
+            const fail = ast.languages.filter(l => !l.available);
+            console.log(`  Status:   ${c.green}active${c.reset}`);
+            console.log(`  Languages: ${ok.join(", ")}`);
+            if (fail.length > 0) {
+                for (const f of fail) {
+                    console.log(`  ${c.yellow}Unavailable: ${f.language} (${f.error})${c.reset}`);
+                }
+            }
+        }
+        else {
+            console.log(`  Status:   ${c.yellow}unavailable${c.reset} (falling back to regex chunking)`);
+            for (const l of ast.languages) {
+                if (l.error)
+                    console.log(`  ${c.dim}${l.language}: ${l.error}${c.reset}`);
+            }
+        }
+    }
+    catch {
+        console.log(`\n${c.bold}AST Chunking${c.reset}`);
+        console.log(`  Status:   ${c.dim}not available${c.reset}`);
+    }
+    if (collections.length > 0) {
+        console.log(`\n${c.bold}Collections${c.reset}`);
+        for (const col of collections) {
+            const lastMod = col.last_modified ? formatTimeAgo(new Date(col.last_modified)) : "never";
+            const contexts = contextsByCollection.get(col.name) || [];
+            console.log(`  ${c.cyan}${col.name}${c.reset} ${c.dim}(qmd://${col.name}/)${c.reset}`);
+            console.log(`    ${c.dim}Pattern:${c.reset}  ${col.glob_pattern}`);
+            console.log(`    ${c.dim}Files:${c.reset}    ${col.active_count} (updated ${lastMod})`);
+            if (contexts.length > 0) {
+                console.log(`    ${c.dim}Contexts:${c.reset} ${contexts.length}`);
+                for (const ctx of contexts) {
+                    // Handle both empty string and '/' as root context
+                    const pathDisplay = (ctx.path_prefix === '' || ctx.path_prefix === '/') ? '/' : `/${ctx.path_prefix}`;
+                    const contextPreview = ctx.context.length > 60
+                        ? ctx.context.substring(0, 57) + '...'
+                        : ctx.context;
+                    console.log(`      ${c.dim}${pathDisplay}:${c.reset} ${contextPreview}`);
+                }
+            }
+        }
+        // Show examples of virtual paths
+        console.log(`\n${c.bold}Examples${c.reset}`);
+        console.log(`  ${c.dim}# List files in a collection${c.reset}`);
+        if (collections.length > 0 && collections[0]) {
+            console.log(`  qmd ls ${collections[0].name}`);
+        }
+        console.log(`  ${c.dim}# Get a document${c.reset}`);
+        if (collections.length > 0 && collections[0]) {
+            console.log(`  qmd get qmd://${collections[0].name}/path/to/file.md`);
+        }
+        console.log(`  ${c.dim}# Search within a collection${c.reset}`);
+        if (collections.length > 0 && collections[0]) {
+            console.log(`  qmd search "query" -c ${collections[0].name}`);
+        }
+    }
+    else {
+        console.log(`\n${c.dim}No collections. Run 'qmd collection add .' to index markdown files.${c.reset}`);
+    }
+    // Models
+    {
+        // hf:org/repo/file.gguf → https://huggingface.co/org/repo
+        const hfLink = (uri) => {
+            const match = uri.match(/^hf:([^/]+\/[^/]+)\//);
+            return match ? `https://huggingface.co/${match[1]}` : uri;
+        };
+        const activeModels = resolveModelsForCli();
+        console.log(`\n${c.bold}Models${c.reset}`);
+        console.log(`  Embedding:   ${hfLink(activeModels.embed)}`);
+        console.log(`  Reranking:   ${hfLink(activeModels.rerank)}`);
+        console.log(`  Generation:  ${hfLink(activeModels.generate)}`);
+    }
+    // Tips section
+    const tips = [];
+    // Check for collections without context
+    const collectionsWithoutContext = collections.filter(col => {
+        const contexts = contextsByCollection.get(col.name) || [];
+        return contexts.length === 0;
+    });
+    if (collectionsWithoutContext.length > 0) {
+        const names = collectionsWithoutContext.map(c => c.name).slice(0, 3).join(', ');
+        const more = collectionsWithoutContext.length > 3 ? ` +${collectionsWithoutContext.length - 3} more` : '';
+        tips.push(`Add context to collections for better search results: ${names}${more}`);
+        tips.push(`  ${c.dim}qmd context add qmd://<name>/ "What this collection contains"${c.reset}`);
+        tips.push(`  ${c.dim}qmd context add qmd://<name>/meeting-notes "Weekly team meeting notes"${c.reset}`);
+    }
+    // Check for collections without update commands
+    const collectionsWithoutUpdate = collections.filter(col => {
+        const yamlCol = getCollectionFromYaml(col.name);
+        return !yamlCol?.update;
+    });
+    if (collectionsWithoutUpdate.length > 0 && collections.length > 1) {
+        const names = collectionsWithoutUpdate.map(c => c.name).slice(0, 3).join(', ');
+        const more = collectionsWithoutUpdate.length > 3 ? ` +${collectionsWithoutUpdate.length - 3} more` : '';
+        tips.push(`Add update commands to keep collections fresh: ${names}${more}`);
+        tips.push(`  ${c.dim}qmd collection update-cmd <name> 'git stash && git pull --rebase --ff-only && git stash pop'${c.reset}`);
+    }
+    if (tips.length > 0) {
+        console.log(`\n${c.bold}Tips${c.reset}`);
+        for (const tip of tips) {
+            console.log(`  ${tip}`);
+        }
+    }
+    closeDb();
+}
+async function updateCollections() {
+    await initializeKuromojiTokenizer(); // kuromoji: morphological analysis for CJK FTS
+    const db = getDb();
+    const storeInstance = getStore();
+    // Collections are defined in YAML; no duplicate cleanup needed.
+    // Clear Ollama cache on update
+    clearCache(db);
+    const collections = listCollections(db);
+    if (collections.length === 0) {
+        console.log(`${c.dim}No collections found. Run 'qmd collection add .' to index markdown files.${c.reset}`);
+        closeDb();
+        return;
+    }
+    console.log(`${c.bold}Updating ${collections.length} collection(s)...${c.reset}\n`);
+    for (let i = 0; i < collections.length; i++) {
+        const col = collections[i];
+        if (!col)
+            continue;
+        console.log(`${c.cyan}[${i + 1}/${collections.length}]${c.reset} ${c.bold}${col.name}${c.reset} ${c.dim}(${col.glob_pattern})${c.reset}`);
+        // Execute custom update command if specified in YAML
+        const yamlCol = getCollectionFromYaml(col.name);
+        if (yamlCol?.update) {
+            console.log(`${c.dim}    Running update command: ${yamlCol.update}${c.reset}`);
+            try {
+                const proc = nodeSpawn("bash", ["-c", yamlCol.update], {
+                    cwd: col.pwd,
+                    stdio: ["ignore", "pipe", "pipe"],
+                });
+                const [output, errorOutput, exitCode] = await new Promise((resolve, reject) => {
+                    let out = "";
+                    let err = "";
+                    proc.stdout?.on("data", (d) => { out += d.toString(); });
+                    proc.stderr?.on("data", (d) => { err += d.toString(); });
+                    proc.on("error", reject);
+                    proc.on("close", (code) => resolve([out, err, code ?? 1]));
+                });
+                if (output.trim()) {
+                    console.log(output.trim().split('\n').map(l => `    ${l}`).join('\n'));
+                }
+                if (errorOutput.trim()) {
+                    console.log(errorOutput.trim().split('\n').map(l => `    ${l}`).join('\n'));
+                }
+                if (exitCode !== 0) {
+                    console.log(`${c.yellow}✗ Update command failed with exit code ${exitCode}${c.reset}`);
+                    process.exit(exitCode);
+                }
+            }
+            catch (err) {
+                console.log(`${c.yellow}✗ Update command failed: ${err}${c.reset}`);
+                process.exit(1);
+            }
+        }
+        const startTime = Date.now();
+        console.log(`Collection: ${col.pwd} (${col.glob_pattern})`);
+        progress.indeterminate();
+        const result = await reindexCollection(storeInstance, col.pwd, col.glob_pattern, col.name, {
+            ignorePatterns: yamlCol?.ignore,
+            onProgress: (info) => {
+                progress.set((info.current / info.total) * 100);
+                const elapsed = (Date.now() - startTime) / 1000;
+                const rate = info.current / elapsed;
+                const remaining = (info.total - info.current) / rate;
+                const eta = info.current > 2 ? ` ETA: ${formatETA(remaining)}` : "";
+                if (isTTY)
+                    process.stderr.write(`\rIndexing: ${info.current}/${info.total}${eta}        `);
+            },
+        });
+        progress.clear();
+        console.log(`\nIndexed: ${result.indexed} new, ${result.updated} updated, ${result.unchanged} unchanged, ${result.removed} removed`);
+        if (result.orphanedCleaned > 0) {
+            console.log(`Cleaned up ${result.orphanedCleaned} orphaned content hash(es)`);
+        }
+        console.log("");
+    }
+    // Check if any documents need embedding (show once at end)
+    const needsEmbedding = getHashesNeedingEmbedding(db);
+    closeDb();
+    console.log(`${c.green}✓ All collections updated.${c.reset}`);
+    if (needsEmbedding > 0) {
+        console.log(`\nRun 'qmd embed' to update embeddings (${needsEmbedding} unique hashes need vectors)`);
+    }
+}
+/**
+ * Detect which collection (if any) contains the given filesystem path.
+ * Returns { collectionId, collectionName, relativePath } or null if not in any collection.
+ */
+function detectCollectionFromPath(db, fsPath) {
+    const realPath = getRealPath(fsPath);
+    // Find collections that this path is under from YAML
+    const allCollections = yamlListCollections();
+    // Find longest matching path
+    let bestMatch = null;
+    for (const coll of allCollections) {
+        if (realPath.startsWith(coll.path + '/') || realPath === coll.path) {
+            if (!bestMatch || coll.path.length > bestMatch.path.length) {
+                bestMatch = { name: coll.name, path: coll.path };
+            }
+        }
+    }
+    if (!bestMatch)
+        return null;
+    // Calculate relative path
+    let relativePath = realPath;
+    if (relativePath.startsWith(bestMatch.path + '/')) {
+        relativePath = relativePath.slice(bestMatch.path.length + 1);
+    }
+    else if (relativePath === bestMatch.path) {
+        relativePath = '';
+    }
+    return {
+        collectionName: bestMatch.name,
+        relativePath
+    };
+}
+async function contextAdd(pathArg, contextText) {
+    const db = getDb();
+    // Handle "/" as global context (applies to all collections)
+    if (pathArg === '/') {
+        setGlobalContext(contextText);
+        resyncConfig();
+        console.log(`${c.green}✓${c.reset} Set global context`);
+        console.log(`${c.dim}Context: ${contextText}${c.reset}`);
+        closeDb();
+        return;
+    }
+    // Resolve path - defaults to current directory if not provided
+    let fsPath = pathArg || '.';
+    if (fsPath === '.' || fsPath === './') {
+        fsPath = getPwd();
+    }
+    else if (fsPath.startsWith('~/')) {
+        fsPath = homedir() + fsPath.slice(1);
+    }
+    else if (!fsPath.startsWith('/') && !fsPath.startsWith('qmd://')) {
+        fsPath = resolve(getPwd(), fsPath);
+    }
+    // Handle virtual paths (qmd://collection/path)
+    if (isVirtualPath(fsPath)) {
+        const parsed = parseVirtualPath(fsPath);
+        if (!parsed) {
+            console.error(`${c.yellow}Invalid virtual path: ${fsPath}${c.reset}`);
+            process.exit(1);
+        }
+        const coll = getCollectionFromYaml(parsed.collectionName);
+        if (!coll) {
+            console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
+            process.exit(1);
+        }
+        yamlAddContext(parsed.collectionName, parsed.path, contextText);
+        resyncConfig();
+        const displayPath = parsed.path
+            ? `qmd://${parsed.collectionName}/${parsed.path}`
+            : `qmd://${parsed.collectionName}/ (collection root)`;
+        console.log(`${c.green}✓${c.reset} Added context for: ${displayPath}`);
+        console.log(`${c.dim}Context: ${contextText}${c.reset}`);
+        closeDb();
+        return;
+    }
+    // Detect collection from filesystem path
+    const detected = detectCollectionFromPath(db, fsPath);
+    if (!detected) {
+        console.error(`${c.yellow}Path is not in any indexed collection: ${fsPath}${c.reset}`);
+        console.error(`${c.dim}Run 'qmd status' to see indexed collections${c.reset}`);
+        process.exit(1);
+    }
+    yamlAddContext(detected.collectionName, detected.relativePath, contextText);
+    resyncConfig();
+    const displayPath = detected.relativePath ? `qmd://${detected.collectionName}/${detected.relativePath}` : `qmd://${detected.collectionName}/`;
+    console.log(`${c.green}✓${c.reset} Added context for: ${displayPath}`);
+    console.log(`${c.dim}Context: ${contextText}${c.reset}`);
+    closeDb();
+}
+function contextList() {
+    const db = getDb();
+    const allContexts = listAllContexts();
+    if (allContexts.length === 0) {
+        console.log(`${c.dim}No contexts configured. Use 'qmd context add' to add one.${c.reset}`);
+        closeDb();
+        return;
+    }
+    console.log(`\n${c.bold}Configured Contexts${c.reset}\n`);
+    let lastCollection = '';
+    for (const ctx of allContexts) {
+        if (ctx.collection !== lastCollection) {
+            console.log(`${c.cyan}${ctx.collection}${c.reset}`);
+            lastCollection = ctx.collection;
+        }
+        const displayPath = ctx.path ? `  ${ctx.path}` : '  / (root)';
+        console.log(`${displayPath}`);
+        console.log(`    ${c.dim}${ctx.context}${c.reset}`);
+    }
+    closeDb();
+}
+function contextRemove(pathArg) {
+    if (pathArg === '/') {
+        // Remove global context
+        setGlobalContext(undefined);
+        // Resync so SQLite store_config is updated
+        const s = getStore();
+        resyncConfig();
+        closeDb();
+        console.log(`${c.green}✓${c.reset} Removed global context`);
+        return;
+    }
+    // Handle virtual paths
+    if (isVirtualPath(pathArg)) {
+        const parsed = parseVirtualPath(pathArg);
+        if (!parsed) {
+            console.error(`${c.yellow}Invalid virtual path: ${pathArg}${c.reset}`);
+            process.exit(1);
+        }
+        const coll = getCollectionFromYaml(parsed.collectionName);
+        if (!coll) {
+            console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
+            process.exit(1);
+        }
+        const success = yamlRemoveContext(coll.name, parsed.path);
+        if (!success) {
+            console.error(`${c.yellow}No context found for: ${pathArg}${c.reset}`);
+            process.exit(1);
+        }
+        console.log(`${c.green}✓${c.reset} Removed context for: ${pathArg}`);
+        return;
+    }
+    // Handle filesystem paths
+    let fsPath = pathArg;
+    if (fsPath === '.' || fsPath === './') {
+        fsPath = getPwd();
+    }
+    else if (fsPath.startsWith('~/')) {
+        fsPath = homedir() + fsPath.slice(1);
+    }
+    else if (!fsPath.startsWith('/')) {
+        fsPath = resolve(getPwd(), fsPath);
+    }
+    const db = getDb();
+    const detected = detectCollectionFromPath(db, fsPath);
+    closeDb();
+    if (!detected) {
+        console.error(`${c.yellow}Path is not in any indexed collection: ${fsPath}${c.reset}`);
+        process.exit(1);
+    }
+    const success = yamlRemoveContext(detected.collectionName, detected.relativePath);
+    if (!success) {
+        console.error(`${c.yellow}No context found for: qmd://${detected.collectionName}/${detected.relativePath}${c.reset}`);
+        process.exit(1);
+    }
+    console.log(`${c.green}✓${c.reset} Removed context for: qmd://${detected.collectionName}/${detected.relativePath}`);
+}
+/**
+ * Render an absolute filesystem path for human display under --full-path.
+ *
+ * If the path is the current working directory or a subpath of it, return a
+ * "./"-prefixed relative path so it is unambiguously a filesystem path (not a
+ * bare collection-relative string that could be confused for a `qmd://`
+ * fragment). Otherwise return the absolute realpath so symlinks resolve
+ * consistently. Returns `null` if the path could not be normalized — callers
+ * fall back to whatever they had before.
+ */
+function renderFullPath(absolutePath, cwd = process.cwd()) {
+    let real;
+    try {
+        real = realpathSync(absolutePath);
+    }
+    catch {
+        real = absolutePath;
+    }
+    const cwdReal = (() => { try {
+        return realpathSync(cwd);
+    }
+    catch {
+        return cwd;
+    } })();
+    if (real === cwdReal)
+        return "./";
+    if (real.startsWith(cwdReal + "/")) {
+        const rel = relativePath(cwdReal, real);
+        if (rel && !rel.startsWith(".."))
+            return `./${rel}`;
+    }
+    return real;
+}
+function getDocument(filename, fromLine, maxLines, lineNumbers, fullPath = false) {
+    // Parse :line suffix from filename. Two forms:
+    //   "file.md:100"     -> start at line 100
+    //   "file.md:100:40"  -> start at line 100, read 40 lines
+    // The :// in virtual paths is never matched because we anchor digits to $.
+    // Explicit --from/-l flags always win over values parsed from the path.
+    let inputPath = filename;
+    const rangeMatch = inputPath.match(/:(\d+):(\d+)$/);
+    if (rangeMatch) {
+        if (fromLine === undefined)
+            fromLine = parseInt(rangeMatch[1], 10);
+        if (maxLines === undefined)
+            maxLines = parseInt(rangeMatch[2], 10);
+        inputPath = inputPath.slice(0, -rangeMatch[0].length);
+    }
+    else {
+        const colonMatch = inputPath.match(/:(\d+)$/);
+        if (colonMatch) {
+            const matched = colonMatch[1];
+            if (matched) {
+                if (fromLine === undefined)
+                    fromLine = parseInt(matched, 10);
+                inputPath = inputPath.slice(0, -colonMatch[0].length);
+            }
+        }
+    }
+    if (fromLine !== undefined)
+        fromLine = Math.max(1, fromLine);
+    const parsedIndexPath = isVirtualPath(inputPath) ? parseVirtualPath(inputPath) : null;
+    if (parsedIndexPath?.indexName) {
+        setIndexName(parsedIndexPath.indexName);
+        setConfigIndexName(parsedIndexPath.indexName);
+    }
+    const db = getDb();
+    // Handle docid lookup (#abc123, abc123, "#abc123", "abc123", etc.)
+    if (isDocid(inputPath)) {
+        const docidMatch = findDocumentByDocid(db, inputPath);
+        if (docidMatch) {
+            inputPath = docidMatch.filepath;
+        }
+        else {
+            console.error(`Document not found: ${filename}`);
+            closeDb();
+            process.exit(1);
+        }
+    }
+    let doc = null;
+    let virtualPath;
+    // Handle virtual paths (qmd://collection/path)
+    if (isVirtualPath(inputPath)) {
+        const parsed = parseVirtualPath(inputPath);
+        if (!parsed) {
+            console.error(`Invalid virtual path: ${inputPath}`);
+            closeDb();
+            process.exit(1);
+        }
+        // Try exact match on collection + path
+        doc = db.prepare(`
+      SELECT d.collection as collectionName, d.path, content.doc as body
+      FROM documents d
+      JOIN content ON content.hash = d.hash
+      WHERE d.collection = ? AND d.path = ? AND d.active = 1
+    `).get(parsed.collectionName, parsed.path);
+        if (!doc) {
+            // Try fuzzy match by path ending
+            doc = db.prepare(`
+        SELECT d.collection as collectionName, d.path, content.doc as body
+        FROM documents d
+        JOIN content ON content.hash = d.hash
+        WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
+        LIMIT 1
+      `).get(parsed.collectionName, `%${parsed.path}`);
+        }
+        virtualPath = inputPath;
+    }
+    else {
+        // Try to interpret as collection/path format first (before filesystem path)
+        // If path is relative (no / or ~ prefix), check if first component is a collection name
+        if (!inputPath.startsWith('/') && !inputPath.startsWith('~')) {
+            const parts = inputPath.split('/');
+            if (parts.length >= 2) {
+                const possibleCollection = parts[0];
+                const possiblePath = parts.slice(1).join('/');
+                // Check if this collection exists
+                const collExists = possibleCollection ? db.prepare(`
+          SELECT 1 FROM documents WHERE collection = ? AND active = 1 LIMIT 1
+        `).get(possibleCollection) : null;
+                if (collExists) {
+                    // Try exact match on collection + path
+                    doc = db.prepare(`
+            SELECT d.collection as collectionName, d.path, 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(possibleCollection || "", possiblePath || "");
+                    if (!doc) {
+                        // Try fuzzy match by path ending
+                        doc = db.prepare(`
+              SELECT d.collection as collectionName, d.path, content.doc as body
+              FROM documents d
+              JOIN content ON content.hash = d.hash
+              WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
+              LIMIT 1
+            `).get(possibleCollection || "", `%${possiblePath}`);
+                    }
+                    if (doc) {
+                        virtualPath = buildVirtualPath(doc.collectionName, doc.path);
+                        // Skip the filesystem path handling below
+                    }
+                }
+            }
+        }
+        // If not found as collection/path, handle as filesystem paths
+        if (!doc) {
+            let fsPath = inputPath;
+            // Expand ~ to home directory
+            if (fsPath.startsWith('~/')) {
+                fsPath = homedir() + fsPath.slice(1);
+            }
+            else if (!fsPath.startsWith('/')) {
+                // Relative path - resolve from current directory
+                fsPath = resolve(getPwd(), fsPath);
+            }
+            fsPath = getRealPath(fsPath);
+            // Try to detect which collection contains this path
+            const detected = detectCollectionFromPath(db, fsPath);
+            if (detected) {
+                // Found collection - query by collection name + relative path
+                doc = db.prepare(`
+          SELECT d.collection as collectionName, d.path, content.doc as body
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE d.collection = ? AND d.path = ? AND d.active = 1
+        `).get(detected.collectionName, detected.relativePath);
+            }
+            // Fuzzy match by filename (last component of path)
+            if (!doc) {
+                const filename = inputPath.split('/').pop() || inputPath;
+                doc = db.prepare(`
+          SELECT d.collection as collectionName, d.path, content.doc as body
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE d.path LIKE ? AND d.active = 1
+          LIMIT 1
+        `).get(`%${filename}`);
+            }
+            if (doc) {
+                virtualPath = buildVirtualPath(doc.collectionName, doc.path);
+            }
+            else {
+                virtualPath = inputPath;
+            }
+        }
+    }
+    // Ensure doc is not null before proceeding
+    if (!doc) {
+        console.error(`Document not found: ${filename}`);
+        closeDb();
+        process.exit(1);
+    }
+    // Get context for this file
+    const context = getContextForPath(db, doc.collectionName, doc.path);
+    // Resolve the docid (first 6 chars of the content hash) so callers always
+    // know what they retrieved and can cite it back to `get`/`multi-get`.
+    const hashRow = db.prepare(`
+    SELECT d.hash as hash
+    FROM documents d
+    WHERE d.collection = ? AND d.path = ? AND d.active = 1
+  `).get(doc.collectionName, doc.path);
+    const docid = hashRow?.hash ? hashRow.hash.slice(0, 6) : undefined;
+    const canonicalPath = buildVirtualPath(doc.collectionName, doc.path);
+    // --full-path: show the on-disk path instead of the qmd:// URL + docid, when
+    // the file actually exists. Fall back to the canonical header otherwise.
+    let header;
+    if (fullPath) {
+        const fsPath = resolveVirtualPath(db, canonicalPath);
+        if (fsPath && existsSync(fsPath)) {
+            header = renderFullPath(fsPath);
+        }
+        else {
+            header = docid ? `${canonicalPath}  #${docid}` : canonicalPath;
+        }
+    }
+    else {
+        header = docid ? `${canonicalPath}  #${docid}` : canonicalPath;
+    }
+    let output = doc.body;
+    const startLine = fromLine || 1;
+    // Apply line filtering if specified
+    if (fromLine !== undefined || maxLines !== undefined) {
+        const lines = output.split('\n');
+        const start = startLine - 1; // Convert to 0-indexed
+        const end = maxLines !== undefined ? start + maxLines : lines.length;
+        output = lines.slice(start, end).join('\n');
+    }
+    // Line numbers are on by default (disable with --no-line-numbers) so the
+    // model can cite exact lines and request follow-up ranges via path:from:count.
+    if (lineNumbers) {
+        output = addLineNumbers(output, startLine);
+    }
+    // Header: identify the document (path + docid, or the on-disk path with
+    // --full-path), then optional context.
+    console.log(header);
+    if (context) {
+        console.log(`Folder Context: ${context}`);
+    }
+    console.log("---\n");
+    console.log(output);
+    closeDb();
+}
+// Multi-get: fetch multiple documents by glob pattern or comma-separated list
+function multiGet(pattern, maxLines, maxBytes = DEFAULT_MULTI_GET_MAX_BYTES, format = "cli", lineNumbers = true, fullPath = false) {
+    const db = getDb();
+    // Check if it's a comma-separated list or a glob pattern
+    const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?') && !pattern.includes('{');
+    let files;
+    if (isCommaSeparated) {
+        // Comma-separated list of files (can be virtual paths or relative paths)
+        const names = pattern.split(',').map(s => s.trim()).filter(Boolean);
+        files = [];
+        for (const name of names) {
+            let doc = null;
+            // Handle virtual paths
+            if (isVirtualPath(name)) {
+                const parsed = parseVirtualPath(name);
+                if (parsed) {
+                    // Try exact match on collection + path
+                    doc = db.prepare(`
+            SELECT
+              'qmd://' || d.collection || '/' || d.path as virtual_path,
+              LENGTH(content.doc) as body_length,
+              d.collection,
+              d.path
+            FROM documents d
+            JOIN content ON content.hash = d.hash
+            WHERE d.collection = ? AND d.path = ? AND d.active = 1
+          `).get(parsed.collectionName, parsed.path);
+                }
+            }
+            else {
+                // Try exact match on path
+                doc = db.prepare(`
+          SELECT
+            'qmd://' || d.collection || '/' || d.path as virtual_path,
+            LENGTH(content.doc) as body_length,
+            d.collection,
+            d.path
+          FROM documents d
+          JOIN content ON content.hash = d.hash
+          WHERE d.path = ? AND d.active = 1
+          LIMIT 1
+        `).get(name);
+                // Try suffix match
+                if (!doc) {
+                    doc = db.prepare(`
+            SELECT
+              'qmd://' || d.collection || '/' || d.path as virtual_path,
+              LENGTH(content.doc) as body_length,
+              d.collection,
+              d.path
+            FROM documents d
+            JOIN content ON content.hash = d.hash
+            WHERE d.path LIKE ? AND d.active = 1
+            LIMIT 1
+          `).get(`%${name}`);
+                }
+            }
+            if (doc) {
+                files.push({
+                    filepath: doc.virtual_path,
+                    displayPath: doc.virtual_path,
+                    bodyLength: doc.body_length,
+                    collection: doc.collection,
+                    path: doc.path
+                });
+            }
+            else {
+                console.error(`File not found: ${name}`);
+            }
+        }
+    }
+    else {
+        // Glob pattern - matchFilesByGlob now returns virtual paths
+        files = matchFilesByGlob(db, pattern).map(f => ({
+            ...f,
+            collection: undefined, // Will be fetched later if needed
+            path: undefined
+        }));
+        if (files.length === 0) {
+            console.error(`No files matched pattern: ${pattern}`);
+            closeDb();
+            process.exit(1);
+        }
+    }
+    // Collect results for structured output
+    const results = [];
+    for (const file of files) {
+        // Parse virtual path to get collection info if not already available
+        let collection = file.collection;
+        let path = file.path;
+        if (!collection || !path) {
+            const parsed = parseVirtualPath(file.filepath);
+            if (parsed) {
+                collection = parsed.collectionName;
+                path = parsed.path;
+            }
+        }
+        // Get context using collection-scoped function
+        const context = collection && path ? getContextForPath(db, collection, path) : null;
+        // Resolve docid (first 6 chars of content hash) so every entry can be cited.
+        const docidRow = collection && path ? db.prepare(`
+      SELECT d.hash as hash
+      FROM documents d
+      WHERE d.collection = ? AND d.path = ? AND d.active = 1
+    `).get(collection, path) : null;
+        const docid = docidRow?.hash ? docidRow.hash.slice(0, 6) : undefined;
+        // --full-path: resolve the on-disk path when it exists (else fall back).
+        // Display as ./-prefixed relative path when under $PWD; absolute realpath
+        // otherwise. See renderFullPath() for the policy.
+        let fsPath;
+        if (fullPath) {
+            const resolved = resolveVirtualPath(db, file.filepath);
+            if (resolved && existsSync(resolved))
+                fsPath = renderFullPath(resolved);
+        }
+        // Check size limit
+        if (file.bodyLength > maxBytes) {
+            results.push({
+                file: file.filepath,
+                displayPath: file.displayPath,
+                fsPath,
+                docid,
+                title: file.displayPath.split('/').pop() || file.displayPath,
+                body: "",
+                context,
+                skipped: true,
+                skipReason: `File too large (${Math.round(file.bodyLength / 1024)}KB > ${Math.round(maxBytes / 1024)}KB). Use 'qmd get ${file.displayPath}' to retrieve.`,
+            });
+            continue;
+        }
+        // Fetch document content using collection and path
+        if (!collection || !path)
+            continue;
+        const doc = db.prepare(`
+      SELECT content.doc as body, d.title
+      FROM documents d
+      JOIN content ON content.hash = d.hash
+      WHERE d.collection = ? AND d.path = ? AND d.active = 1
+    `).get(collection, path);
+        if (!doc)
+            continue;
+        let body = doc.body;
+        // Apply line limit if specified
+        if (maxLines !== undefined) {
+            const lines = body.split('\n');
+            body = lines.slice(0, maxLines).join('\n');
+            if (lines.length > maxLines) {
+                body += `\n\n[... truncated ${lines.length - maxLines} more lines]`;
+            }
+        }
+        // Line numbers on by default (disable with --no-line-numbers).
+        if (lineNumbers) {
+            body = addLineNumbers(body);
+        }
+        results.push({
+            file: file.filepath,
+            displayPath: file.displayPath,
+            fsPath,
+            docid,
+            title: doc.title || file.displayPath.split('/').pop() || file.displayPath,
+            body,
+            context,
+            skipped: false,
+        });
+    }
+    closeDb();
+    // --full-path replaces the qmd:// path + docid with the on-disk path (when it
+    // resolved). Per result: pick the identifier and whether to show the docid.
+    const identOf = (r) => (fullPath && r.fsPath) ? r.fsPath : r.displayPath;
+    const docidOf = (r) => (fullPath && r.fsPath) ? undefined : r.docid;
+    // Output based on format
+    if (format === "json") {
+        const output = results.map(r => {
+            const docidVal = docidOf(r);
+            return {
+                file: identOf(r),
+                ...(docidVal && { docid: `#${docidVal}` }),
+                title: r.title,
+                ...(r.context && { context: r.context }),
+                ...(r.skipped ? { skipped: true, reason: r.skipReason } : { body: r.body }),
+            };
+        });
+        console.log(JSON.stringify(output, null, 2));
+    }
+    else if (format === "csv") {
+        const escapeField = (val) => {
+            if (val === null || val === undefined)
+                return "";
+            const str = String(val);
+            if (str.includes(",") || str.includes('"') || str.includes("\n")) {
+                return `"${str.replace(/"/g, '""')}"`;
+            }
+            return str;
+        };
+        console.log("docid,file,title,context,skipped,body");
+        for (const r of results) {
+            const docidVal = docidOf(r);
+            console.log([docidVal ? `#${docidVal}` : "", identOf(r), r.title, r.context, r.skipped ? "true" : "false", r.skipped ? r.skipReason : r.body].map(escapeField).join(","));
+        }
+    }
+    else if (format === "files") {
+        for (const r of results) {
+            const docidVal = docidOf(r);
+            const id = docidVal ? `#${docidVal} ` : "";
+            const ctx = r.context ? `,"${r.context.replace(/"/g, '""')}"` : "";
+            const status = r.skipped ? "[SKIPPED]" : "";
+            console.log(`${id}${identOf(r)}${ctx}${status ? `,${status}` : ""}`);
+        }
+    }
+    else if (format === "md") {
+        for (const r of results) {
+            const docidVal = docidOf(r);
+            console.log(`## ${identOf(r)}\n`);
+            if (docidVal)
+                console.log(`**docid:** \`#${docidVal}\`\n`);
+            if (r.title && r.title !== r.displayPath)
+                console.log(`**Title:** ${r.title}\n`);
+            if (r.context)
+                console.log(`**Context:** ${r.context}\n`);
+            if (r.skipped) {
+                console.log(`> ${r.skipReason}\n`);
+            }
+            else {
+                console.log("```");
+                console.log(r.body);
+                console.log("```\n");
+            }
+        }
+    }
+    else if (format === "xml") {
+        console.log('<?xml version="1.0" encoding="UTF-8"?>');
+        console.log("<documents>");
+        for (const r of results) {
+            const docidVal = docidOf(r);
+            const docidAttr = docidVal ? ` docid="#${docidVal}"` : "";
+            console.log(`  <document${docidAttr}>`);
+            console.log(`    <file>${escapeXml(identOf(r))}</file>`);
+            console.log(`    <title>${escapeXml(r.title)}</title>`);
+            if (r.context)
+                console.log(`    <context>${escapeXml(r.context)}</context>`);
+            if (r.skipped) {
+                console.log(`    <skipped>true</skipped>`);
+                console.log(`    <reason>${escapeXml(r.skipReason || "")}</reason>`);
+            }
+            else {
+                console.log(`    <body>${escapeXml(r.body)}</body>`);
+            }
+            console.log("  </document>");
+        }
+        console.log("</documents>");
+    }
+    else {
+        // CLI format (default)
+        for (const r of results) {
+            const docidVal = docidOf(r);
+            const id = docidVal ? `  #${docidVal}` : "";
+            console.log(`\n${'='.repeat(60)}`);
+            console.log(`File: ${identOf(r)}${id}`);
+            console.log(`${'='.repeat(60)}\n`);
+            if (r.skipped) {
+                console.log(`[SKIPPED: ${r.skipReason}]`);
+                continue;
+            }
+            if (r.context) {
+                console.log(`Folder Context: ${r.context}\n---\n`);
+            }
+            console.log(r.body);
+        }
+    }
+}
+// List files in virtual file tree
+function listFiles(pathArg) {
+    const db = getDb();
+    if (!pathArg) {
+        // No argument - list all collections
+        const yamlCollections = yamlListCollections();
+        if (yamlCollections.length === 0) {
+            console.log("No collections found. Run 'qmd collection add .' to index files.");
+            closeDb();
+            return;
+        }
+        // Get file counts from database for each collection
+        const collections = yamlCollections.map(coll => {
+            const stats = db.prepare(`
+        SELECT COUNT(*) as file_count
+        FROM documents d
+        WHERE d.collection = ? AND d.active = 1
+      `).get(coll.name);
+            return {
+                name: coll.name,
+                file_count: stats?.file_count || 0
+            };
+        });
+        console.log(`${c.bold}Collections:${c.reset}\n`);
+        for (const coll of collections) {
+            console.log(`  ${c.dim}qmd://${c.reset}${c.cyan}${coll.name}/${c.reset}  ${c.dim}(${coll.file_count} files)${c.reset}`);
+        }
+        closeDb();
+        return;
+    }
+    // Parse the path argument
+    let collectionName;
+    let pathPrefix = null;
+    const afterScheme = pathArg.startsWith('qmd://') ? pathArg.slice('qmd://'.length) : null;
+    if (afterScheme !== null && afterScheme.startsWith('/')) {
+        // Absolute-path collection: qmd:///Users/foo/bar — normalizeVirtualPath would corrupt
+        // this by stripping all leading slashes, so bypass parseVirtualPath entirely.
+        const normalized = afterScheme.replace(/\/$/, '');
+        const allColls = yamlListCollections();
+        const match = allColls
+            .filter(c => normalized === c.name || normalized.startsWith(c.name + '/'))
+            .sort((a, b) => b.name.length - a.name.length)[0];
+        if (match) {
+            collectionName = match.name;
+            const rest = normalized.slice(match.name.length).replace(/^\//, '');
+            pathPrefix = rest || null;
+        }
+        else {
+            // Preserve the historical qmd:////collection/path alias behavior for normal
+            // collections when no absolute-path collection matches.
+            const parsed = parseVirtualPath(pathArg);
+            if (!parsed) {
+                console.error(`Invalid virtual path: ${pathArg}`);
+                closeDb();
+                process.exit(1);
+            }
+            collectionName = parsed.collectionName;
+            pathPrefix = parsed.path;
+        }
+    }
+    else if (afterScheme !== null) {
+        // Normal virtual path: qmd://collection-name/path
+        const parsed = parseVirtualPath(pathArg);
+        if (!parsed) {
+            console.error(`Invalid virtual path: ${pathArg}`);
+            closeDb();
+            process.exit(1);
+        }
+        collectionName = parsed.collectionName;
+        pathPrefix = parsed.path;
+    }
+    else if (pathArg.startsWith('/')) {
+        // Raw absolute filesystem path — longest-prefix match against collection names
+        const normalized = pathArg.replace(/\/$/, '');
+        const allColls = yamlListCollections();
+        const match = allColls
+            .filter(c => normalized === c.name || normalized.startsWith(c.name + '/'))
+            .sort((a, b) => b.name.length - a.name.length)[0];
+        if (match) {
+            collectionName = match.name;
+            const rest = normalized.slice(match.name.length).replace(/^\//, '');
+            pathPrefix = rest || null;
+        }
+        else {
+            collectionName = normalized;
+        }
+    }
+    else {
+        // Short collection name or name/path
+        const parts = pathArg.split('/');
+        collectionName = parts[0] || '';
+        if (parts.length > 1) {
+            pathPrefix = parts.slice(1).join('/');
+        }
+    }
+    // Get the collection
+    const coll = getCollectionFromYaml(collectionName);
+    if (!coll) {
+        console.error(`Collection not found: ${collectionName}`);
+        console.error(`Run 'qmd ls' to see available collections.`);
+        closeDb();
+        process.exit(1);
+    }
+    // List files in the collection with size and modification time
+    let query;
+    let params;
+    if (pathPrefix) {
+        // List files under a specific path
+        query = `
+      SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
+      FROM documents d
+      JOIN content ct ON d.hash = ct.hash
+      WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
+      ORDER BY d.path
+    `;
+        params = [coll.name, `${pathPrefix}%`];
+    }
+    else {
+        // List all files in the collection
+        query = `
+      SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
+      FROM documents d
+      JOIN content ct ON d.hash = ct.hash
+      WHERE d.collection = ? AND d.active = 1
+      ORDER BY d.path
+    `;
+        params = [coll.name];
+    }
+    const files = db.prepare(query).all(...params);
+    if (files.length === 0) {
+        if (pathPrefix) {
+            console.log(`No files found under qmd://${collectionName}/${pathPrefix}`);
+        }
+        else {
+            console.log(`No files found in collection: ${collectionName}`);
+        }
+        closeDb();
+        return;
+    }
+    // Calculate max widths for alignment
+    const maxSize = Math.max(...files.map(f => formatBytes(f.size).length));
+    // Output in ls -l style
+    for (const file of files) {
+        const sizeStr = formatBytes(file.size).padStart(maxSize);
+        const date = new Date(file.modified_at);
+        const timeStr = formatLsTime(date);
+        // Dim the qmd:// prefix, highlight the filename
+        console.log(`${sizeStr}  ${timeStr}  ${c.dim}qmd://${collectionName}/${c.reset}${c.cyan}${file.path}${c.reset}`);
+    }
+    closeDb();
+}
+// Format date/time like ls -l
+function formatLsTime(date) {
+    const now = new Date();
+    const sixMonthsAgo = new Date(now.getTime() - 6 * 30 * 24 * 60 * 60 * 1000);
+    const months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec'];
+    const month = months[date.getMonth()];
+    const day = date.getDate().toString().padStart(2, ' ');
+    // If file is older than 6 months, show year instead of time
+    if (date < sixMonthsAgo) {
+        const year = date.getFullYear();
+        return `${month} ${day}  ${year}`;
+    }
+    else {
+        const hours = date.getHours().toString().padStart(2, '0');
+        const minutes = date.getMinutes().toString().padStart(2, '0');
+        return `${month} ${day} ${hours}:${minutes}`;
+    }
+}
+// Collection management commands
+function collectionList() {
+    const db = getDb();
+    const collections = listCollections(db);
+    if (collections.length === 0) {
+        console.log("No collections found. Run 'qmd collection add .' to create one.");
+        closeDb();
+        return;
+    }
+    console.log(`${c.bold}Collections (${collections.length}):${c.reset}\n`);
+    for (const coll of collections) {
+        const updatedAt = coll.last_modified ? new Date(coll.last_modified) : new Date();
+        const timeAgo = formatTimeAgo(updatedAt);
+        // Get YAML config to check includeByDefault
+        const yamlColl = getCollectionFromYaml(coll.name);
+        const excluded = yamlColl?.includeByDefault === false;
+        const excludeTag = excluded ? ` ${c.yellow}[excluded]${c.reset}` : '';
+        console.log(`${c.cyan}${coll.name}${c.reset} ${c.dim}(qmd://${coll.name}/)${c.reset}${excludeTag}`);
+        console.log(`  ${c.dim}Pattern:${c.reset}  ${coll.glob_pattern}`);
+        if (yamlColl?.ignore?.length) {
+            console.log(`  ${c.dim}Ignore:${c.reset}   ${yamlColl.ignore.join(', ')}`);
+        }
+        console.log(`  ${c.dim}Files:${c.reset}    ${coll.active_count}`);
+        console.log(`  ${c.dim}Updated:${c.reset}  ${timeAgo}`);
+        console.log();
+    }
+    closeDb();
+}
+async function collectionAdd(pwd, globPattern, name) {
+    // If name not provided, generate from pwd basename
+    let collName = name;
+    if (!collName) {
+        const parts = pwd.split('/').filter(Boolean);
+        collName = parts[parts.length - 1] || 'root';
+    }
+    // Check if collection with this name already exists in YAML
+    const existing = getCollectionFromYaml(collName);
+    if (existing) {
+        console.error(`${c.yellow}Collection '${collName}' already exists.${c.reset}`);
+        console.error(`Use a different name with --name <name>`);
+        process.exit(1);
+    }
+    // Check if a collection with this pwd+glob already exists in YAML
+    const allCollections = yamlListCollections();
+    const existingPwdGlob = allCollections.find(c => c.path === pwd && c.pattern === globPattern);
+    if (existingPwdGlob) {
+        console.error(`${c.yellow}A collection already exists for this path and pattern:${c.reset}`);
+        console.error(`  Name: ${existingPwdGlob.name} (qmd://${existingPwdGlob.name}/)`);
+        console.error(`  Pattern: ${globPattern}`);
+        console.error(`\nUse 'qmd update' to re-index it, or remove it first with 'qmd collection remove ${existingPwdGlob.name}'`);
+        process.exit(1);
+    }
+    // Add to YAML config + sync to SQLite
+    const { addCollection } = await import("../collections.js");
+    addCollection(collName, pwd, globPattern);
+    resyncConfig();
+    // Create the collection and index files
+    console.log(`Creating collection '${collName}'...`);
+    const newColl = getCollectionFromYaml(collName);
+    await indexFiles(pwd, globPattern, collName, false, newColl?.ignore);
+    console.log(`${c.green}✓${c.reset} Collection '${collName}' created successfully`);
+}
+function collectionRemove(name) {
+    // Check if collection exists in YAML
+    const coll = getCollectionFromYaml(name);
+    if (!coll) {
+        console.error(`${c.yellow}Collection not found: ${name}${c.reset}`);
+        console.error(`Run 'qmd collection list' to see available collections.`);
+        process.exit(1);
+    }
+    const db = getDb();
+    const result = removeCollection(db, name);
+    // Also remove from YAML config
+    yamlRemoveCollectionFn(name);
+    closeDb();
+    console.log(`${c.green}✓${c.reset} Removed collection '${name}'`);
+    console.log(`  Deleted ${result.deletedDocs} documents`);
+    if (result.cleanedHashes > 0) {
+        console.log(`  Cleaned up ${result.cleanedHashes} orphaned content hashes`);
+    }
+}
+function collectionRename(oldName, newName) {
+    // Check if old collection exists in YAML
+    const coll = getCollectionFromYaml(oldName);
+    if (!coll) {
+        console.error(`${c.yellow}Collection not found: ${oldName}${c.reset}`);
+        console.error(`Run 'qmd collection list' to see available collections.`);
+        process.exit(1);
+    }
+    // Check if new name already exists in YAML
+    const existing = getCollectionFromYaml(newName);
+    if (existing) {
+        console.error(`${c.yellow}Collection name already exists: ${newName}${c.reset}`);
+        console.error(`Choose a different name or remove the existing collection first.`);
+        process.exit(1);
+    }
+    const db = getDb();
+    renameCollection(db, oldName, newName);
+    // Also rename in YAML config
+    yamlRenameCollectionFn(oldName, newName);
+    closeDb();
+    console.log(`${c.green}✓${c.reset} Renamed collection '${oldName}' to '${newName}'`);
+    console.log(`  Virtual paths updated: ${c.cyan}qmd://${oldName}/${c.reset} → ${c.cyan}qmd://${newName}/${c.reset}`);
+}
+async function indexFiles(pwd, globPattern = DEFAULT_GLOB, collectionName, suppressEmbedNotice = false, ignorePatterns) {
+    const db = getDb();
+    const resolvedPwd = pwd || getPwd();
+    const now = new Date().toISOString();
+    const excludeDirs = ["node_modules", ".git", ".cache", "vendor", "dist", "build"];
+    // Clear Ollama cache on index
+    clearCache(db);
+    // Collection name must be provided (from YAML)
+    if (!collectionName) {
+        throw new Error("Collection name is required. Collections must be defined in ~/.config/qmd/index.yml");
+    }
+    console.log(`Collection: ${resolvedPwd} (${globPattern})`);
+    progress.indeterminate();
+    const allIgnore = [
+        ...excludeDirs.map(d => `**/${d}/**`),
+        ...(ignorePatterns || []),
+    ];
+    const allFiles = await fastGlob(globPattern, {
+        cwd: resolvedPwd,
+        onlyFiles: true,
+        followSymbolicLinks: false,
+        dot: false,
+        ignore: allIgnore,
+    });
+    // Filter hidden files/folders (dot: false handles top-level but not nested)
+    const files = allFiles.filter(file => {
+        const parts = file.split("/");
+        return !parts.some(part => part.startsWith("."));
+    });
+    const total = files.length;
+    const hasNoFiles = total === 0;
+    if (hasNoFiles) {
+        progress.clear();
+        console.log("No files found matching pattern.");
+        // Continue so the deactivation pass can mark previously indexed docs as inactive.
+    }
+    let indexed = 0, updated = 0, unchanged = 0, processed = 0;
+    const seenPaths = new Set();
+    const startTime = Date.now();
+    for (const relativeFile of files) {
+        const filepath = getRealPath(resolve(resolvedPwd, relativeFile));
+        // Store the literal relative path — handelize() is NOT applied at index time.
+        const path = relativeFile.replace(/\\/g, '/');
+        seenPaths.add(path);
+        let content;
+        try {
+            content = readFileSync(filepath, "utf-8");
+        }
+        catch {
+            // Skip files that can't be read (e.g. iCloud evicted files returning EAGAIN)
+            processed++;
+            progress.set((processed / total) * 100);
+            continue;
+        }
+        // Skip empty files - nothing useful to index
+        if (!content.trim()) {
+            processed++;
+            continue;
+        }
+        const hash = await hashContent(content);
+        const title = extractTitle(content, relativeFile);
+        // Check if document exists (also migrates legacy lowercase paths)
+        const existing = findOrMigrateLegacyDocument(db, collectionName, path);
+        if (existing) {
+            if (existing.hash === hash) {
+                // Hash unchanged, but check if title needs updating
+                if (existing.title !== title) {
+                    updateDocumentTitle(db, existing.id, title, now);
+                    updated++;
+                }
+                else {
+                    unchanged++;
+                }
+            }
+            else {
+                // Content changed - insert new content hash and update document
+                insertContent(db, hash, content, now);
+                const stat = statSync(filepath);
+                updateDocument(db, existing.id, title, hash, stat ? new Date(stat.mtime).toISOString() : now);
+                updated++;
+            }
+        }
+        else {
+            // New document - insert content and document
+            indexed++;
+            insertContent(db, hash, content, now);
+            const stat = statSync(filepath);
+            insertDocument(db, collectionName, path, title, hash, stat ? new Date(stat.birthtime).toISOString() : now, stat ? new Date(stat.mtime).toISOString() : now);
+        }
+        processed++;
+        progress.set((processed / total) * 100);
+        const elapsed = (Date.now() - startTime) / 1000;
+        const rate = processed / elapsed;
+        const remaining = (total - processed) / rate;
+        const eta = processed > 2 ? ` ETA: ${formatETA(remaining)}` : "";
+        if (isTTY)
+            process.stderr.write(`\rIndexing: ${processed}/${total}${eta}        `);
+    }
+    // Deactivate documents in this collection that no longer exist
+    const allActive = getActiveDocumentPaths(db, collectionName);
+    let removed = 0;
+    for (const path of allActive) {
+        if (!seenPaths.has(path)) {
+            deactivateDocument(db, collectionName, path);
+            removed++;
+        }
+    }
+    // Clean up orphaned content hashes (content not referenced by any document)
+    const orphanedContent = cleanupOrphanedContent(db);
+    // Check if vector index needs updating
+    const needsEmbedding = getHashesNeedingEmbedding(db);
+    progress.clear();
+    console.log(`\nIndexed: ${indexed} new, ${updated} updated, ${unchanged} unchanged, ${removed} removed`);
+    if (orphanedContent > 0) {
+        console.log(`Cleaned up ${orphanedContent} orphaned content hash(es)`);
+    }
+    if (needsEmbedding > 0 && !suppressEmbedNotice) {
+        console.log(`\nRun 'qmd embed' to update embeddings (${needsEmbedding} unique hashes need vectors)`);
+    }
+    closeDb();
+}
+function renderProgressBar(percent, width = 30) {
+    const filled = Math.round((percent / 100) * width);
+    const empty = width - filled;
+    const bar = "█".repeat(filled) + "░".repeat(empty);
+    return bar;
+}
+function parseEmbedBatchOption(name, value) {
+    if (value === undefined)
+        return undefined;
+    const parsed = Number(value);
+    if (!Number.isInteger(parsed) || parsed < 1) {
+        throw new Error(`${name} must be a positive integer`);
+    }
+    return parsed;
+}
+function parseChunkStrategy(value) {
+    if (value === undefined)
+        return undefined;
+    const s = String(value);
+    if (s === "auto" || s === "regex")
+        return s;
+    throw new Error(`--chunk-strategy must be "auto" or "regex" (got "${s}")`);
+}
+function ensureModelsConfiguredForCli() {
+    try {
+        const config = loadConfig();
+        const models = resolveModels(config.models);
+        const current = config.models ?? {};
+        if (current.embed !== models.embed || current.generate !== models.generate || current.rerank !== models.rerank) {
+            saveConfig({
+                ...config,
+                models: {
+                    ...current,
+                    embed: models.embed,
+                    generate: models.generate,
+                    rerank: models.rerank,
+                },
+            });
+        }
+        return models;
+    }
+    catch {
+        return resolveModels();
+    }
+}
+export function resolveEmbedModelForCli() {
+    return ensureModelsConfiguredForCli().embed;
+}
+export function resolveGenerateModelForCli() {
+    return ensureModelsConfiguredForCli().generate;
+}
+export function resolveRerankModelForCli() {
+    return ensureModelsConfiguredForCli().rerank;
+}
+function resolveModelsForCli() {
+    return ensureModelsConfiguredForCli();
+}
+async function vectorIndex(model = resolveEmbedModelForCli(), force = false, batchOptions) {
+    const storeInstance = getStore();
+    const db = storeInstance.db;
+    if (force) {
+        console.log(`${c.yellow}Force re-indexing: clearing all vectors...${c.reset}`);
+    }
+    // Check if there's work to do before starting
+    const hashesToEmbed = getHashesNeedingEmbedding(db, batchOptions?.collection, model);
+    if (hashesToEmbed === 0 && !force) {
+        console.log(`${c.green}✓ All content hashes already have embeddings.${c.reset}`);
+        closeDb();
+        return;
+    }
+    console.log(`${c.dim}Model: ${shortModelName(model)}${c.reset}\n`);
+    if (batchOptions?.maxDocsPerBatch !== undefined || batchOptions?.maxBatchBytes !== undefined) {
+        const maxDocsPerBatch = batchOptions.maxDocsPerBatch ?? DEFAULT_EMBED_MAX_DOCS_PER_BATCH;
+        const maxBatchBytes = batchOptions.maxBatchBytes ?? DEFAULT_EMBED_MAX_BATCH_BYTES;
+        console.log(`${c.dim}Batch: ${maxDocsPerBatch} docs / ${formatBytes(maxBatchBytes)}${c.reset}\n`);
+    }
+    cursor.hide();
+    progress.indeterminate();
+    const startTime = Date.now();
+    const result = await generateEmbeddings(storeInstance, {
+        force,
+        model,
+        collection: batchOptions?.collection,
+        maxDocsPerBatch: batchOptions?.maxDocsPerBatch,
+        maxBatchBytes: batchOptions?.maxBatchBytes,
+        chunkStrategy: batchOptions?.chunkStrategy,
+        onProgress: (info) => {
+            if (info.totalBytes === 0)
+                return;
+            // Progress is measured by input bytes, not by chunks. The final chunk
+            // count is discovered lazily batch-by-batch, so displaying
+            // chunksEmbedded/totalChunks makes the percent look wrong when a few
+            // large documents remain. Show chunks as a count and label the byte
+            // percentage explicitly as input progress.
+            const percent = Math.min(100, (info.bytesProcessed / info.totalBytes) * 100);
+            progress.set(percent);
+            const elapsed = (Date.now() - startTime) / 1000;
+            const bytesPerSec = elapsed > 0 ? info.bytesProcessed / elapsed : 0;
+            const remainingBytes = Math.max(0, info.totalBytes - info.bytesProcessed);
+            const etaSec = bytesPerSec > 0 ? remainingBytes / bytesPerSec : Number.POSITIVE_INFINITY;
+            const bar = renderProgressBar(percent);
+            const percentStr = percent.toFixed(0).padStart(3);
+            const throughput = bytesPerSec > 0 ? `${formatBytes(bytesPerSec)}/s` : ".../s";
+            const eta = elapsed > 2 && Number.isFinite(etaSec) ? formatETA(etaSec) : "...";
+            const inputStr = `${formatBytes(info.bytesProcessed)}/${formatBytes(info.totalBytes)} input`;
+            const chunkStr = `${formatCount(info.chunksEmbedded)} chunks`;
+            const errStr = info.errors > 0 ? ` ${c.yellow}${formatCount(info.errors)} err${c.reset}` : "";
+            if (isTTY)
+                process.stderr.write(`\r${c.cyan}${bar}${c.reset} ${c.bold}${percentStr}% input${c.reset} ${c.dim}${chunkStr}${errStr} · ${inputStr} · ${throughput} · ETA ${eta}${c.reset}   `);
+        },
+    });
+    progress.clear();
+    cursor.show();
+    const totalTimeSec = result.durationMs / 1000;
+    if (result.chunksEmbedded === 0 && result.docsProcessed === 0) {
+        console.log(`${c.green}✓ No non-empty documents to embed.${c.reset}`);
+    }
+    else {
+        console.log(`\r${c.green}${renderProgressBar(100)}${c.reset} ${c.bold}100%${c.reset}                                    `);
+        console.log(`\n${c.green}✓ Done!${c.reset} Embedded ${c.bold}${result.chunksEmbedded}${c.reset} chunks from ${c.bold}${result.docsProcessed}${c.reset} documents in ${c.bold}${formatETA(totalTimeSec)}${c.reset}`);
+        if (result.errors > 0) {
+            console.log(`${c.yellow}⚠ ${formatCount(result.errors)} chunks still failed after retries${c.reset}`);
+            for (const failure of (result.failures ?? []).slice(0, 8)) {
+                console.log(`  ${c.dim}${failure.path}#${failure.seq} (${failure.attempts} attempts): ${failure.reason}${c.reset}`);
+            }
+            if ((result.failures?.length ?? 0) > 8) {
+                console.log(`  ${c.dim}...and ${formatCount((result.failures?.length ?? 0) - 8)} more${c.reset}`);
+            }
+        }
+    }
+    closeDb();
+}
+// Sanitize a term for FTS5: remove punctuation except apostrophes
+function sanitizeFTS5Term(term) {
+    // Remove all non-alphanumeric except apostrophes (for contractions like "don't")
+    return term.replace(/[^\w']/g, '').trim();
+}
+// Build FTS5 query: phrase-aware with fallback to individual terms
+function buildFTS5Query(query) {
+    // Sanitize the full query for phrase matching
+    const sanitizedQuery = query.replace(/[^\w\s']/g, '').trim();
+    const terms = query
+        .split(/\s+/)
+        .map(sanitizeFTS5Term)
+        .filter(term => term.length >= 2); // Skip single chars and empty
+    if (terms.length === 0)
+        return "";
+    if (terms.length === 1)
+        return `"${terms[0].replace(/"/g, '""')}"`;
+    // Strategy: exact phrase OR proximity match OR individual terms
+    // Exact phrase matches rank highest, then close proximity, then any term
+    const phrase = `"${sanitizedQuery.replace(/"/g, '""')}"`;
+    const quotedTerms = terms.map(t => `"${t.replace(/"/g, '""')}"`);
+    // FTS5 NEAR syntax: NEAR(term1 term2, distance)
+    const nearPhrase = `NEAR(${quotedTerms.join(' ')}, 10)`;
+    const orTerms = quotedTerms.join(' OR ');
+    // Exact phrase > proximity > any term
+    return `(${phrase}) OR (${nearPhrase}) OR (${orTerms})`;
+}
+// Normalize BM25 score to 0-1 range using sigmoid
+function normalizeBM25(score) {
+    // BM25 scores are negative in SQLite (lower = better)
+    // Typical range: -15 (excellent) to -2 (weak match)
+    // Map to 0-1 where higher is better
+    const absScore = Math.abs(score);
+    // Sigmoid-ish normalization: maps ~2-15 range to ~0.1-0.95
+    return 1 / (1 + Math.exp(-(absScore - 5) / 3));
+}
+// Highlight query terms in text (skip short words < 3 chars)
+function highlightTerms(text, query) {
+    if (!useColor)
+        return text;
+    const terms = query.toLowerCase().split(/\s+/).filter(t => t.length >= 3);
+    let result = text;
+    for (const term of terms) {
+        const regex = new RegExp(`(${term.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')})`, 'gi');
+        result = result.replace(regex, `${c.yellow}${c.bold}$1${c.reset}`);
+    }
+    return result;
+}
+// Format score with color based on value
+function formatScore(score) {
+    const pct = (score * 100).toFixed(0).padStart(3);
+    if (!useColor)
+        return `${pct}%`;
+    if (score >= 0.7)
+        return `${c.green}${pct}%${c.reset}`;
+    if (score >= 0.4)
+        return `${c.yellow}${pct}%${c.reset}`;
+    return `${c.dim}${pct}%${c.reset}`;
+}
+function formatExplainNumber(value) {
+    return value.toFixed(4);
+}
+// Shorten directory path for display - relative to $HOME (used for context paths, not documents)
+function shortPath(dirpath) {
+    const home = homedir();
+    if (dirpath.startsWith(home)) {
+        return '~' + dirpath.slice(home.length);
+    }
+    return dirpath;
+}
+// Emit format-safe empty output for search commands.
+function printEmptySearchResults(format, reason = "no_results") {
+    if (format === "json") {
+        console.log("[]");
+        return;
+    }
+    if (format === "csv") {
+        console.log("docid,score,file,title,context,line,snippet");
+        return;
+    }
+    if (format === "xml") {
+        console.log("<results></results>");
+        return;
+    }
+    if (format === "md" || format === "files") {
+        return;
+    }
+    if (reason === "min_score") {
+        console.log("No results found above minimum score threshold.");
+        return;
+    }
+    console.log("No results found.");
+}
+const DEFAULT_EDITOR_URI_TEMPLATE = "vscode://file/{path}:{line}:{col}";
+function encodePathForEditorUri(absolutePath) {
+    return encodeURI(absolutePath)
+        .replace(/\?/g, "%3F")
+        .replace(/#/g, "%23");
+}
+function getEditorUriTemplate() {
+    const envTemplate = process.env.QMD_EDITOR_URI?.trim();
+    if (envTemplate)
+        return envTemplate;
+    try {
+        const config = loadConfig();
+        const configTemplate = (config.editor_uri
+            || config.editor_uri_template
+            || config.editorUri
+            || (typeof config["editor-uri"] === "string" ? config["editor-uri"] : undefined))?.trim();
+        if (configTemplate)
+            return configTemplate;
+    }
+    catch {
+        // Ignore config parsing issues and use default template.
+    }
+    return DEFAULT_EDITOR_URI_TEMPLATE;
+}
+export function buildEditorUri(template, absolutePath, line, col) {
+    const safeLine = Number.isFinite(line) && line > 0 ? Math.floor(line) : 1;
+    const safeCol = Number.isFinite(col) && col > 0 ? Math.floor(col) : 1;
+    const encodedPath = encodePathForEditorUri(absolutePath);
+    return template
+        .replace(/\{path\}/g, encodedPath)
+        .replace(/\{line\}/g, String(safeLine))
+        .replace(/\{col\}/g, String(safeCol))
+        .replace(/\{column\}/g, String(safeCol));
+}
+export function termLink(text, url, isTTY = !!process.stdout.isTTY) {
+    if (!isTTY)
+        return text;
+    return `\x1b]8;;${url}\x07${text}\x1b]8;;\x07`;
+}
+function outputResults(results, query, opts) {
+    const filtered = results.filter(r => r.score >= opts.minScore).slice(0, opts.limit);
+    if (filtered.length === 0) {
+        printEmptySearchResults(opts.format, "min_score");
+        return;
+    }
+    // Helper to create qmd:// URI from displayPath
+    const toQmdPath = (displayPath) => {
+        const [collectionName, ...segments] = displayPath.split("/");
+        if (!collectionName || segments.length === 0) {
+            return `qmd://${displayPath}`;
+        }
+        const indexName = getActiveIndexName();
+        return buildVirtualPath(collectionName, segments.join("/"), indexName === "index" ? undefined : indexName);
+    };
+    // Helper to pick the visible path for a result. With --full-path we swap
+    // the qmd:// URI for the file's on-disk path via renderFullPath() (./-
+    // prefixed relative when under $PWD, absolute realpath otherwise). Falls
+    // back to qmd:// if the file is no longer resolvable on disk.
+    const linkDbForPaths = opts.fullPath ? getDb() : null;
+    const displayPathFor = (row) => {
+        // Always rebuild from displayPath so the active index name is included
+        // as ?index=… for non-default indexes. row.file may not carry it.
+        const qmdUri = toQmdPath(row.displayPath);
+        if (!opts.fullPath || !linkDbForPaths)
+            return qmdUri;
+        const absolute = resolveVirtualPath(linkDbForPaths, qmdUri);
+        if (!absolute || !existsSync(absolute))
+            return qmdUri;
+        return renderFullPath(absolute);
+    };
+    if (opts.format === "json") {
+        // JSON output for LLM consumption
+        const output = filtered.map(row => {
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);
+            const snippetInfo = extractSnippet(row.body, query, 300, row.chunkPos, row.chunkLen, opts.intent);
+            let body = opts.full ? row.body : undefined;
+            let snippet = !opts.full ? snippetInfo.snippet : undefined;
+            if (opts.lineNumbers) {
+                if (body)
+                    body = addLineNumbers(body);
+                if (snippet)
+                    snippet = addLineNumbers(snippet);
+            }
+            // With --full-path, omit docid (the on-disk path is the identifier).
+            return {
+                ...(docid && !opts.fullPath && { docid: `#${docid}` }),
+                score: Math.round(row.score * 100) / 100,
+                file: displayPathFor(row),
+                line: snippetInfo.line,
+                title: row.title,
+                ...(row.context && { context: row.context }),
+                ...(body && { body }),
+                ...(snippet && { snippet }),
+                ...(opts.explain && row.explain && { explain: row.explain }),
+            };
+        });
+        console.log(JSON.stringify(output, null, 2));
+    }
+    else if (opts.format === "files") {
+        // Simple docid,score,filepath,context output
+        for (const row of filtered) {
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
+            const ctx = row.context ? `,"${row.context.replace(/"/g, '""')}"` : "";
+            if (opts.fullPath) {
+                // --full-path: drop the docid, the on-disk path is the identifier.
+                console.log(`${row.score.toFixed(2)},${displayPathFor(row)}${ctx}`);
+            }
+            else {
+                console.log(`#${docid},${row.score.toFixed(2)},${displayPathFor(row)}${ctx}`);
+            }
+        }
+    }
+    else if (opts.format === "cli") {
+        const editorUriTemplate = getEditorUriTemplate();
+        const linkDb = getDb();
+        for (let i = 0; i < filtered.length; i++) {
+            const row = filtered[i];
+            if (!row)
+                continue;
+            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent);
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);
+            // Line 1: filepath with docid
+            // Default: show the full qmd:// URI so the user can see which collection
+            // a hit lives in and can pipe the same string straight back into
+            // `qmd get`. A bare collection-relative path like `sources/foo.md` is
+            // ambiguous: it's not a real filesystem path, not a URI, and not a
+            // shell-friendly identifier on its own.
+            // With --full-path the visible label is the file's on-disk path
+            // ($PWD-relative when in a subfolder; absolute realpath otherwise),
+            // and the docid is omitted because the path is the identifier.
+            const virtualPath = toQmdPath(row.displayPath);
+            const parsed = parseVirtualPath(virtualPath);
+            const absolutePath = resolveVirtualPath(linkDb, virtualPath);
+            const visiblePath = displayPathFor(row);
+            // Only show :line if we actually found a term match in the snippet body (exclude header line).
+            const snippetBody = snippet.split("\n").slice(1).join("\n").toLowerCase();
+            const hasMatch = query.toLowerCase().split(/\s+/).some(t => t.length > 0 && snippetBody.includes(t));
+            const lineInfo = hasMatch ? `:${line}` : "";
+            const docidStr = (docid && !opts.fullPath) ? ` ${c.dim}#${docid}${c.reset}` : "";
+            if (process.stdout.isTTY && absolutePath && parsed?.path) {
+                const linkLine = hasMatch ? line : 1;
+                const linkTarget = buildEditorUri(editorUriTemplate, absolutePath, linkLine, 1);
+                const clickable = termLink(`${visiblePath}${lineInfo}`, linkTarget);
+                console.log(`${c.cyan}${clickable}${c.reset}${docidStr}`);
+            }
+            else {
+                console.log(`${c.cyan}${visiblePath}${c.dim}${lineInfo}${c.reset}${docidStr}`);
+            }
+            // Line 2: Title (if available)
+            if (row.title) {
+                console.log(`${c.bold}Title: ${row.title}${c.reset}`);
+            }
+            // Line 3: Context (if available)
+            if (row.context) {
+                console.log(`${c.dim}Context: ${row.context}${c.reset}`);
+            }
+            // Line 4: Score
+            const score = formatScore(row.score);
+            console.log(`Score: ${c.bold}${score}${c.reset}`);
+            if (opts.explain && row.explain) {
+                const explain = row.explain;
+                const ftsScores = explain.ftsScores.length > 0
+                    ? explain.ftsScores.map(formatExplainNumber).join(", ")
+                    : "none";
+                const vecScores = explain.vectorScores.length > 0
+                    ? explain.vectorScores.map(formatExplainNumber).join(", ")
+                    : "none";
+                const contribSummary = explain.rrf.contributions
+                    .slice()
+                    .sort((a, b) => b.rrfContribution - a.rrfContribution)
+                    .slice(0, 3)
+                    .map(c => `${c.source}/${c.queryType}#${c.rank}:${formatExplainNumber(c.rrfContribution)}`)
+                    .join(" | ");
+                console.log(`${c.dim}Explain: fts=[${ftsScores}] vec=[${vecScores}]${c.reset}`);
+                console.log(`${c.dim}  RRF: total=${formatExplainNumber(explain.rrf.totalScore)} base=${formatExplainNumber(explain.rrf.baseScore)} bonus=${formatExplainNumber(explain.rrf.topRankBonus)} rank=${explain.rrf.rank}${c.reset}`);
+                console.log(`${c.dim}  Blend: ${Math.round(explain.rrf.weight * 100)}%*${formatExplainNumber(explain.rrf.positionScore)} + ${Math.round((1 - explain.rrf.weight) * 100)}%*${formatExplainNumber(explain.rerankScore)} = ${formatExplainNumber(explain.blendedScore)}${c.reset}`);
+                if (contribSummary.length > 0) {
+                    console.log(`${c.dim}  Top RRF contributions: ${contribSummary}${c.reset}`);
+                }
+            }
+            console.log();
+            // Snippet with highlighting (diff-style header included)
+            const content = opts.full ? row.body : snippet;
+            const displayContent = opts.lineNumbers ? addLineNumbers(content, opts.full ? 1 : line) : content;
+            const highlighted = highlightTerms(displayContent, query);
+            console.log(highlighted);
+            // Double empty line between results
+            if (i < filtered.length - 1)
+                console.log('\n');
+        }
+    }
+    else if (opts.format === "md") {
+        for (let i = 0; i < filtered.length; i++) {
+            const row = filtered[i];
+            if (!row)
+                continue;
+            const visiblePath = displayPathFor(row);
+            const heading = row.title || visiblePath;
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);
+            let content = opts.full ? row.body : extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent).snippet;
+            if (opts.lineNumbers) {
+                content = addLineNumbers(content);
+            }
+            const fileLine = `**file:** \`${visiblePath}\`\n`;
+            // With --full-path the on-disk path is the identifier; drop the docid line.
+            const docidLine = (docid && !opts.fullPath) ? `**docid:** \`#${docid}\`\n` : "";
+            const contextLine = row.context ? `**context:** ${row.context}\n` : "";
+            console.log(`---\n# ${heading}\n${fileLine}${docidLine}${contextLine}\n${content}\n`);
+        }
+    }
+    else if (opts.format === "xml") {
+        for (const row of filtered) {
+            const titleAttr = row.title ? ` title="${row.title.replace(/"/g, '&quot;')}"` : "";
+            const contextAttr = row.context ? ` context="${row.context.replace(/"/g, '&quot;')}"` : "";
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
+            let content = opts.full ? row.body : extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent).snippet;
+            if (opts.lineNumbers) {
+                content = addLineNumbers(content);
+            }
+            const docidAttr = opts.fullPath ? "" : ` docid="#${docid}"`;
+            console.log(`<file${docidAttr} name="${displayPathFor(row)}"${titleAttr}${contextAttr}>\n${content}\n</file>\n`);
+        }
+    }
+    else {
+        // CSV format
+        const csvHeader = opts.fullPath
+            ? "score,file,title,context,line,snippet"
+            : "docid,score,file,title,context,line,snippet";
+        console.log(csvHeader);
+        for (const row of filtered) {
+            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent);
+            let content = opts.full ? row.body : snippet;
+            if (opts.lineNumbers) {
+                content = addLineNumbers(content, opts.full ? 1 : line);
+            }
+            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
+            const snippetText = content || "";
+            const path = escapeCSV(displayPathFor(row));
+            const tail = `${path},${escapeCSV(row.title || "")},${escapeCSV(row.context || "")},${line},${escapeCSV(snippetText)}`;
+            if (opts.fullPath) {
+                console.log(`${row.score.toFixed(4)},${tail}`);
+            }
+            else {
+                console.log(`#${docid},${row.score.toFixed(4)},${tail}`);
+            }
+        }
+    }
+}
+// Resolve -c collection filter: supports single string, array, or undefined.
+// Returns validated collection names (exits on unknown collection).
+function resolveCollectionFilter(raw, useDefaults = false) {
+    // If no filter specified and useDefaults is true, use default collections
+    if (!raw && useDefaults) {
+        return getDefaultCollectionNames();
+    }
+    if (!raw)
+        return [];
+    const names = Array.isArray(raw) ? raw : [raw];
+    const validated = [];
+    for (const name of names) {
+        const coll = getCollectionFromYaml(name);
+        if (!coll) {
+            console.error(`Collection not found: ${name}`);
+            closeDb();
+            process.exit(1);
+        }
+        validated.push(name);
+    }
+    return validated;
+}
+// Post-filter results to only include files from specified collections.
+function filterByCollections(results, collectionNames) {
+    if (collectionNames.length <= 1)
+        return results;
+    const prefixes = collectionNames.map(n => `qmd://${n}/`);
+    return results.filter(r => {
+        const path = r.filepath || r.file || '';
+        return prefixes.some(p => path.startsWith(p));
+    });
+}
+function parseStructuredQuery(query) {
+    const rawLines = query.split('\n').map((line, idx) => ({
+        raw: line,
+        trimmed: line.trim(),
+        number: idx + 1,
+    })).filter(line => line.trimmed.length > 0);
+    if (rawLines.length === 0)
+        return null;
+    const prefixRe = /^(lex|vec|hyde):\s*/i;
+    const expandRe = /^expand:\s*/i;
+    const intentRe = /^intent:\s*/i;
+    const typed = [];
+    let intent;
+    for (const line of rawLines) {
+        if (expandRe.test(line.trimmed)) {
+            if (rawLines.length > 1) {
+                throw new Error(`Line ${line.number} starts with expand:, but query documents cannot mix expand with typed lines. Submit a single expand query instead.`);
+            }
+            const text = line.trimmed.replace(expandRe, '').trim();
+            if (!text) {
+                throw new Error('expand: query must include text.');
+            }
+            return null; // treat as standalone expand query
+        }
+        // Parse intent: lines
+        if (intentRe.test(line.trimmed)) {
+            if (intent !== undefined) {
+                throw new Error(`Line ${line.number}: only one intent: line is allowed per query document.`);
+            }
+            const text = line.trimmed.replace(intentRe, '').trim();
+            if (!text) {
+                throw new Error(`Line ${line.number}: intent: must include text.`);
+            }
+            intent = text;
+            continue;
+        }
+        const match = line.trimmed.match(prefixRe);
+        if (match) {
+            const type = match[1].toLowerCase();
+            const text = line.trimmed.slice(match[0].length).trim();
+            if (!text) {
+                throw new Error(`Line ${line.number} (${type}:) must include text.`);
+            }
+            if (/\r|\n/.test(text)) {
+                throw new Error(`Line ${line.number} (${type}:) contains a newline. Keep each query on a single line.`);
+            }
+            typed.push({ type, query: text, line: line.number });
+            continue;
+        }
+        if (rawLines.length === 1) {
+            // Single plain line -> implicit expand
+            return null;
+        }
+        throw new Error(`Line ${line.number} is missing a lex:/vec:/hyde:/intent: prefix. Each line in a query document must start with one.`);
+    }
+    // intent: alone is not a valid query — must have at least one search
+    if (intent && typed.length === 0) {
+        throw new Error('intent: cannot appear alone. Add at least one lex:, vec:, or hyde: line.');
+    }
+    return typed.length > 0 ? { searches: typed, intent } : null;
+}
+function search(query, opts) {
+    const db = getDb();
+    // Validate collection filter (supports multiple -c flags)
+    // Use default collections if none specified
+    const collectionNames = resolveCollectionFilter(opts.collection, true);
+    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
+    // Use large limit for --all, otherwise fetch more than needed and let outputResults filter
+    const fetchLimit = opts.all ? 100000 : Math.max(50, opts.limit * 2);
+    const results = filterByCollections(searchFTS(db, query, fetchLimit, singleCollection), collectionNames);
+    // Add context to results
+    const resultsWithContext = results.map(r => ({
+        file: r.filepath,
+        displayPath: r.displayPath,
+        title: r.title,
+        body: r.body || "",
+        score: r.score,
+        context: getContextForFile(db, r.filepath),
+        hash: r.hash,
+        docid: r.docid,
+    }));
+    closeDb();
+    if (resultsWithContext.length === 0) {
+        printEmptySearchResults(opts.format);
+        return;
+    }
+    outputResults(resultsWithContext, query, opts);
+}
+// Log query expansion as a tree to stderr (CLI progress feedback)
+function logExpansionTree(originalQuery, expanded) {
+    const lines = [];
+    lines.push(`${c.dim}├─ ${originalQuery}${c.reset}`);
+    for (const q of expanded) {
+        let preview = q.query.replace(/\n/g, ' ');
+        if (preview.length > 72)
+            preview = preview.substring(0, 69) + '...';
+        lines.push(`${c.dim}├─ ${q.type}: ${preview}${c.reset}`);
+    }
+    if (lines.length > 0) {
+        lines[lines.length - 1] = lines[lines.length - 1].replace('├─', '└─');
+    }
+    for (const line of lines)
+        process.stderr.write(line + '\n');
+}
+async function vectorSearch(query, opts, _model = DEFAULT_EMBED_MODEL) {
+    const store = getStore();
+    // Validate collection filter (supports multiple -c flags)
+    // Use default collections if none specified
+    const collectionNames = resolveCollectionFilter(opts.collection, true);
+    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
+    checkIndexHealth(store.db);
+    await withLLMSession(async () => {
+        let results = await vectorSearchQuery(store, query, {
+            collection: singleCollection,
+            limit: opts.all ? 500 : (opts.limit || 10),
+            minScore: opts.minScore || 0.3,
+            intent: opts.intent,
+            hooks: {
+                onExpand: (original, expanded) => {
+                    logExpansionTree(original, expanded);
+                    process.stderr.write(`${c.dim}Searching ${expanded.length + 1} vector queries...${c.reset}\n`);
+                },
+            },
+        });
+        // Post-filter for multi-collection
+        if (collectionNames.length > 1) {
+            results = results.filter(r => {
+                const prefixes = collectionNames.map(n => `qmd://${n}/`);
+                return prefixes.some(p => r.file.startsWith(p));
+            });
+        }
+        closeDb();
+        if (results.length === 0) {
+            printEmptySearchResults(opts.format);
+            return;
+        }
+        outputResults(results.map(r => ({
+            file: r.file,
+            displayPath: r.displayPath,
+            title: r.title,
+            body: r.body,
+            score: r.score,
+            context: r.context,
+            docid: r.docid,
+        })), query, { ...opts, limit: results.length });
+    }, { maxDuration: 10 * 60 * 1000, name: 'vectorSearch' });
+}
+async function querySearch(query, opts, _embedModel = DEFAULT_EMBED_MODEL, _rerankModel = DEFAULT_RERANK_MODEL) {
+    const store = getStore();
+    // Validate collection filter (supports multiple -c flags)
+    // Use default collections if none specified
+    const collectionNames = resolveCollectionFilter(opts.collection, true);
+    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
+    checkIndexHealth(store.db);
+    // Check for structured query syntax (lex:/vec:/hyde:/intent: prefixes)
+    const parsed = parseStructuredQuery(query);
+    // Intent can come from --intent flag or from intent: line in query document
+    const intent = opts.intent || parsed?.intent;
+    await withLLMSession(async () => {
+        let results;
+        if (parsed) {
+            const structuredQueries = parsed.searches;
+            // Structured search — user provided their own query expansions
+            const typeLabels = structuredQueries.map(s => s.type).join('+');
+            process.stderr.write(`${c.dim}Structured search: ${structuredQueries.length} queries (${typeLabels})${c.reset}\n`);
+            if (intent) {
+                process.stderr.write(`${c.dim}├─ intent: ${intent}${c.reset}\n`);
+            }
+            // Log each sub-query
+            for (const s of structuredQueries) {
+                let preview = s.query.replace(/\n/g, ' ');
+                if (preview.length > 72)
+                    preview = preview.substring(0, 69) + '...';
+                process.stderr.write(`${c.dim}├─ ${s.type}: ${preview}${c.reset}\n`);
+            }
+            process.stderr.write(`${c.dim}└─ Searching...${c.reset}\n`);
+            results = await structuredSearch(store, structuredQueries, {
+                collections: singleCollection ? [singleCollection] : undefined,
+                limit: opts.all ? 500 : (opts.limit || 10),
+                minScore: opts.minScore || 0,
+                candidateLimit: opts.candidateLimit,
+                skipRerank: opts.skipRerank,
+                explain: !!opts.explain,
+                intent,
+                chunkStrategy: opts.chunkStrategy,
+                hooks: {
+                    onEmbedStart: (count) => {
+                        process.stderr.write(`${c.dim}Embedding ${count} ${count === 1 ? 'query' : 'queries'}...${c.reset}`);
+                    },
+                    onEmbedDone: (ms) => {
+                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
+                    },
+                    onRerankStart: (chunkCount) => {
+                        process.stderr.write(`${c.dim}Reranking ${chunkCount} chunks...${c.reset}`);
+                        progress.indeterminate();
+                    },
+                    onRerankDone: (ms) => {
+                        progress.clear();
+                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
+                    },
+                },
+            });
+        }
+        else {
+            // Standard hybrid query with automatic expansion
+            results = await hybridQuery(store, query, {
+                collection: singleCollection,
+                limit: opts.all ? 500 : (opts.limit || 10),
+                minScore: opts.minScore || 0,
+                candidateLimit: opts.candidateLimit,
+                skipRerank: opts.skipRerank,
+                explain: !!opts.explain,
+                intent,
+                chunkStrategy: opts.chunkStrategy,
+                hooks: {
+                    onStrongSignal: (score) => {
+                        process.stderr.write(`${c.dim}Strong BM25 signal (${score.toFixed(2)}) — skipping expansion${c.reset}\n`);
+                    },
+                    onExpandStart: () => {
+                        process.stderr.write(`${c.dim}Expanding query...${c.reset}`);
+                    },
+                    onExpand: (original, expanded, ms) => {
+                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
+                        logExpansionTree(original, expanded);
+                        process.stderr.write(`${c.dim}Searching ${expanded.length + 1} queries...${c.reset}\n`);
+                    },
+                    onEmbedStart: (count) => {
+                        process.stderr.write(`${c.dim}Embedding ${count} ${count === 1 ? 'query' : 'queries'}...${c.reset}`);
+                    },
+                    onEmbedDone: (ms) => {
+                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
+                    },
+                    onRerankStart: (chunkCount) => {
+                        process.stderr.write(`${c.dim}Reranking ${chunkCount} chunks...${c.reset}`);
+                        progress.indeterminate();
+                    },
+                    onRerankDone: (ms) => {
+                        progress.clear();
+                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
+                    },
+                },
+            });
+        }
+        // Post-filter for multi-collection
+        if (collectionNames.length > 1) {
+            results = results.filter(r => {
+                const prefixes = collectionNames.map(n => `qmd://${n}/`);
+                return prefixes.some(p => r.file.startsWith(p));
+            });
+        }
+        closeDb();
+        if (results.length === 0) {
+            printEmptySearchResults(opts.format);
+            return;
+        }
+        // Use first lex/vec query for output context, or original query
+        const structuredQueries = parsed?.searches;
+        const displayQuery = structuredQueries
+            ? (structuredQueries.find(s => s.type === 'lex')?.query || structuredQueries.find(s => s.type === 'vec')?.query || query)
+            : query;
+        outputResults(results.map(r => ({
+            file: r.file,
+            displayPath: r.displayPath,
+            title: r.title,
+            body: r.body,
+            chunkPos: r.bestChunkPos,
+            chunkLen: r.bestChunk.length,
+            score: r.score,
+            context: r.context,
+            docid: r.docid,
+            explain: r.explain,
+        })), displayQuery, { ...opts, limit: results.length });
+    }, { maxDuration: 10 * 60 * 1000, name: 'querySearch' });
+}
+// Parse CLI arguments using util.parseArgs
+function parseCLI() {
+    const { values, positionals } = parseArgs({
+        args: process.argv.slice(2), // Skip node and script path
+        options: {
+            // Global options
+            index: {
+                type: "string",
+            },
+            context: {
+                type: "string",
+            },
+            help: { type: "boolean", short: "h" },
+            version: { type: "boolean", short: "v" },
+            skill: { type: "boolean" },
+            global: { type: "boolean" },
+            yes: { type: "boolean" },
+            // Search options
+            n: { type: "string" },
+            "min-score": { type: "string" },
+            all: { type: "boolean" },
+            full: { type: "boolean" },
+            format: { type: "string" }, // preferred: --format cli|json|csv|md|xml|files
+            // Legacy boolean format aliases. Kept working for back-compat but
+            // omitted from the documented help; prefer `--format <kind>`.
+            csv: { type: "boolean" },
+            md: { type: "boolean" },
+            xml: { type: "boolean" },
+            files: { type: "boolean" },
+            json: { type: "boolean" },
+            explain: { type: "boolean" },
+            collection: { type: "string", short: "c", multiple: true }, // Filter by collection(s)
+            // Collection options
+            name: { type: "string" }, // collection name
+            mask: { type: "string" }, // glob pattern
+            // Embed options
+            force: { type: "boolean", short: "f" },
+            "max-docs-per-batch": { type: "string" },
+            "max-batch-mb": { type: "string" },
+            // Update options
+            pull: { type: "boolean" }, // git pull before update
+            refresh: { type: "boolean" },
+            // Get options
+            l: { type: "string" }, // max lines
+            from: { type: "string" }, // start line
+            "max-bytes": { type: "string" }, // max bytes for multi-get
+            "line-numbers": { type: "boolean" }, // add line numbers to output (search; default on for get/multi-get)
+            "no-line-numbers": { type: "boolean" }, // disable line numbers for get/multi-get
+            "full-path": { type: "boolean" }, // show on-disk paths instead of qmd:// (get/multi-get/search/query)
+            // Query options
+            "candidate-limit": { type: "string", short: "C" },
+            "no-rerank": { type: "boolean", default: false },
+            "no-gpu": { type: "boolean", default: false },
+            intent: { type: "string" },
+            // Chunking options
+            "chunk-strategy": { type: "string" }, // "regex" (default) or "auto" (AST for code files)
+            // MCP HTTP transport options
+            http: { type: "boolean" },
+            daemon: { type: "boolean" },
+            port: { type: "string" },
+        },
+        allowPositionals: true,
+        strict: false, // Allow unknown options to pass through
+    });
+    if (values["no-gpu"]) {
+        process.env.QMD_FORCE_CPU = "1";
+    }
+    // Select index name (default: "index"). If no explicit --index is supplied,
+    // a project-local .qmd/index.yaml overrides the global config/cache paths.
+    const indexName = values.index;
+    if (indexName) {
+        setIndexName(indexName);
+        setConfigIndexName(indexName);
+        setConfigSource();
+    }
+    else {
+        const localConfigPath = findLocalConfigPath();
+        if (localConfigPath) {
+            setConfigSource({ configPath: localConfigPath });
+            storeDbPathOverride = getLocalDbPath(localConfigPath);
+            closeDb();
+        }
+        else {
+            setConfigSource();
+        }
+    }
+    // Determine output format. Prefer --format <kind>; fall back to the
+    // legacy boolean aliases (--csv/--md/--xml/--files/--json) which remain
+    // wired up for back-compat but are no longer documented.
+    let format = "cli";
+    const rawFormat = typeof values.format === "string" ? values.format.toLowerCase().trim() : "";
+    const VALID_FORMATS = ["cli", "json", "csv", "md", "xml", "files"];
+    if (rawFormat) {
+        if (VALID_FORMATS.includes(rawFormat)) {
+            format = rawFormat;
+        }
+        else {
+            console.error(`Unknown --format value: ${values.format}`);
+            console.error(`Valid: ${VALID_FORMATS.join(", ")}`);
+            process.exit(1);
+        }
+    }
+    else if (values.csv)
+        format = "csv";
+    else if (values.md)
+        format = "md";
+    else if (values.xml)
+        format = "xml";
+    else if (values.files)
+        format = "files";
+    else if (values.json)
+        format = "json";
+    // Default limit: 20 for --files/--json, 5 otherwise
+    // --all means return all results (use very large limit)
+    const defaultLimit = (format === "files" || format === "json") ? 20 : 5;
+    const isAll = !!values.all;
+    const opts = {
+        format,
+        full: !!values.full,
+        limit: isAll ? 100000 : (values.n ? parseInt(String(values.n), 10) || defaultLimit : defaultLimit),
+        minScore: values["min-score"] ? parseFloat(String(values["min-score"])) || 0 : 0,
+        all: isAll,
+        collection: values.collection,
+        lineNumbers: !!values["line-numbers"],
+        candidateLimit: values["candidate-limit"] ? parseInt(String(values["candidate-limit"]), 10) : undefined,
+        skipRerank: !!values["no-rerank"],
+        explain: !!values.explain,
+        intent: values.intent,
+        chunkStrategy: parseChunkStrategy(values["chunk-strategy"]),
+        fullPath: !!values["full-path"],
+    };
+    return {
+        command: positionals[0] || "",
+        args: positionals.slice(1),
+        query: positionals.slice(1).join(" "),
+        opts,
+        values,
+    };
+}
+function getSkillInstallDir(globalInstall) {
+    return globalInstall
+        ? resolve(homedir(), ".agents", "skills", "qmd")
+        : resolve(getPwd(), ".agents", "skills", "qmd");
+}
+function getClaudeSkillLinkPath(globalInstall) {
+    return globalInstall
+        ? resolve(homedir(), ".claude", "skills", "qmd")
+        : resolve(getPwd(), ".claude", "skills", "qmd");
+}
+function pathExists(path) {
+    try {
+        lstatSync(path);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+function removePath(path) {
+    const stat = lstatSync(path);
+    if (stat.isDirectory() && !stat.isSymbolicLink()) {
+        rmSync(path, { recursive: true, force: true });
+    }
+    else {
+        unlinkSync(path);
+    }
+}
+const SKILL_DIR = "skills";
+function findPackageRoot() {
+    if (process.env.QMD_SKILLS_DIR) {
+        return null;
+    }
+    const start = dirname(fileURLToPath(import.meta.url));
+    let current = start;
+    while (true) {
+        if (existsSync(resolve(current, SKILL_DIR))) {
+            return current;
+        }
+        const parent = dirname(current);
+        if (parent === current)
+            break;
+        current = parent;
+    }
+    return null;
+}
+function getSkillSearchDirs(_runtimeOnly = false) {
+    if (process.env.QMD_SKILLS_DIR) {
+        return [process.env.QMD_SKILLS_DIR];
+    }
+    const root = findPackageRoot();
+    if (!root)
+        return [];
+    const dir = resolve(root, SKILL_DIR);
+    return existsSync(dir) ? [dir] : [];
+}
+function parseSkillFrontmatter(content) {
+    const trimmed = content.trimStart();
+    if (!trimmed.startsWith("---"))
+        return null;
+    const end = trimmed.slice(3).indexOf("\n---");
+    if (end < 0)
+        return null;
+    const frontmatter = trimmed.slice(3, 3 + end);
+    let name = "";
+    let description = "";
+    let hidden = false;
+    const lines = frontmatter.split(/\r?\n/);
+    for (let i = 0; i < lines.length; i++) {
+        const line = lines[i];
+        if (line.startsWith("name:")) {
+            name = line.slice("name:".length).trim();
+        }
+        else if (line.startsWith("description:")) {
+            const parts = [line.slice("description:".length).trim()];
+            while (i + 1 < lines.length && /^\s+\S/.test(lines[i + 1])) {
+                i++;
+                parts.push(lines[i].trim());
+            }
+            description = parts.join(" ");
+        }
+        else if (line.startsWith("hidden:")) {
+            const value = line.slice("hidden:".length).trim().toLowerCase();
+            hidden = value === "true" || value === "yes";
+        }
+    }
+    if (!name)
+        return null;
+    return { name, description, hidden };
+}
+function discoverSkills(runtimeOnly = false) {
+    const skills = [];
+    for (const dir of getSkillSearchDirs(runtimeOnly)) {
+        let entries = [];
+        try {
+            entries = readdirSync(dir);
+        }
+        catch {
+            continue;
+        }
+        for (const entry of entries) {
+            const skillDir = resolve(dir, entry);
+            const skillPath = resolve(skillDir, "SKILL.md");
+            if (!existsSync(skillPath))
+                continue;
+            let content = "";
+            try {
+                content = readFileSync(skillPath, "utf-8");
+            }
+            catch {
+                continue;
+            }
+            const parsed = parseSkillFrontmatter(content);
+            if (!parsed)
+                continue;
+            skills.push({ ...parsed, dir: skillDir });
+        }
+    }
+    return skills.sort((a, b) => a.name.localeCompare(b.name));
+}
+function findSkill(name, runtimeOnly = false) {
+    return discoverSkills(runtimeOnly).find((skill) => skill.name === name) ?? null;
+}
+function readSkillContent(skill) {
+    return readFileSync(resolve(skill.dir, "SKILL.md"), "utf-8");
+}
+function collectSkillFiles(skill) {
+    const files = [];
+    for (const subdirName of ["references", "templates", "scripts"]) {
+        const subdir = resolve(skill.dir, subdirName);
+        if (!existsSync(subdir))
+            continue;
+        for (const entry of readdirSync(subdir).sort()) {
+            const filePath = resolve(subdir, entry);
+            try {
+                if (!statSync(filePath).isFile())
+                    continue;
+                files.push({ relativePath: `${subdirName}/${basename(filePath)}`, content: readFileSync(filePath, "utf-8") });
+            }
+            catch {
+                // Ignore unreadable supplementary files.
+            }
+        }
+    }
+    return files;
+}
+function showSkill() {
+    const skill = findSkill("qmd");
+    if (!skill) {
+        throw new Error("QMD skill not found. Reinstall qmd or set QMD_SKILLS_DIR.");
+    }
+    console.log("QMD Skill");
+    console.log("");
+    const content = readSkillContent(skill);
+    process.stdout.write(content.endsWith("\n") ? content : content + "\n");
+}
+function copyDirectoryContents(sourceDir, targetDir) {
+    mkdirSync(targetDir, { recursive: true });
+    for (const entry of readdirSync(sourceDir)) {
+        const sourcePath = resolve(sourceDir, entry);
+        const targetPath = resolve(targetDir, entry);
+        const stat = statSync(sourcePath);
+        if (stat.isDirectory()) {
+            copyDirectoryContents(sourcePath, targetPath);
+        }
+        else if (stat.isFile()) {
+            copyFileSync(sourcePath, targetPath);
+        }
+    }
+}
+function installedSkillStubContent() {
+    return `---
+name: qmd
+description: Bootstrap QMD search instructions from the installed qmd CLI. Use when users ask to find notes, retrieve documents, inspect a wiki, or answer from indexed local markdown.
+license: MIT
+compatibility: Requires qmd CLI. Run \`qmd skill show\` for version-matched instructions.
+allowed-tools: Bash(qmd:*), mcp__qmd__*
+---
+
+# QMD - Query Markdown Documents
+
+This installed skill is intentionally a small bootstrap so it does not go stale
+when the qmd package updates.
+
+Load the full, version-matched QMD instructions from the CLI:
+
+!\`qmd skill show\`
+
+If your agent does not support bang-command expansion, run:
+
+\`\`\`bash
+qmd skill show
+\`\`\`
+
+Then follow those instructions. In short: search first, fetch full sources with
+\`qmd get\` or \`qmd multi-get\`, and answer from retrieved text rather than snippets.
+`;
+}
+function writeSkillInstall(targetDir, force) {
+    if (pathExists(targetDir)) {
+        if (!force) {
+            throw new Error(`Skill already exists: ${targetDir} (use --force to replace it)`);
+        }
+        removePath(targetDir);
+    }
+    const skill = findSkill("qmd");
+    if (!skill) {
+        throw new Error("QMD skill not found. Reinstall qmd or set QMD_SKILLS_DIR.");
+    }
+    copyDirectoryContents(skill.dir, targetDir);
+    writeFileSync(resolve(targetDir, "SKILL.md"), installedSkillStubContent(), "utf-8");
+}
+function outputSkillsJson(payload) {
+    console.log(JSON.stringify(payload));
+}
+function runSkillsCommand(args, jsonMode, fullOption = false, allOption = false) {
+    const subcommand = args[0] ?? "list";
+    const runtimeSkills = () => discoverSkills(true).filter((skill) => !skill.hidden);
+    switch (subcommand) {
+        case "list": {
+            const skills = runtimeSkills();
+            if (jsonMode) {
+                outputSkillsJson({ success: true, data: skills.map(({ name, description }) => ({ name, description })) });
+                return;
+            }
+            if (skills.length === 0) {
+                console.log("No skills found");
+                return;
+            }
+            const maxName = Math.max(...skills.map((skill) => skill.name.length));
+            for (const skill of skills) {
+                console.log(`  ${skill.name.padEnd(maxName)}  ${skill.description}`);
+            }
+            return;
+        }
+        case "get": {
+            const full = fullOption || args.includes("--full");
+            const getAll = allOption || args.includes("--all");
+            const names = args.slice(1).filter((arg) => arg !== "--full" && arg !== "--all");
+            const targets = getAll ? runtimeSkills() : names.map((name) => {
+                const skill = findSkill(name, true);
+                if (!skill) {
+                    throw new Error(`Skill not found: ${name}`);
+                }
+                return skill;
+            });
+            if (targets.length === 0) {
+                throw new Error("No skill name provided. Usage: qmd skills get <name>");
+            }
+            if (jsonMode) {
+                outputSkillsJson({
+                    success: true,
+                    data: targets.map((skill) => ({
+                        name: skill.name,
+                        content: readSkillContent(skill),
+                        ...(full ? { files: collectSkillFiles(skill).map((file) => ({ path: file.relativePath, content: file.content })) } : {}),
+                    })),
+                });
+                return;
+            }
+            targets.forEach((skill, index) => {
+                if (index > 0)
+                    console.log("\n---\n");
+                const content = readSkillContent(skill);
+                process.stdout.write(content.endsWith("\n") ? content : content + "\n");
+                if (full) {
+                    for (const file of collectSkillFiles(skill)) {
+                        console.log(`\n--- ${file.relativePath} ---\n`);
+                        process.stdout.write(file.content.endsWith("\n") ? file.content : file.content + "\n");
+                    }
+                }
+            });
+            return;
+        }
+        case "path": {
+            const name = args[1];
+            if (!name) {
+                const paths = getSkillSearchDirs(true);
+                if (jsonMode)
+                    outputSkillsJson({ success: true, data: { paths } });
+                else
+                    paths.forEach((path) => console.log(path));
+                return;
+            }
+            const skill = findSkill(name, true);
+            if (!skill) {
+                throw new Error(`Skill not found: ${name}`);
+            }
+            if (jsonMode)
+                outputSkillsJson({ success: true, data: { name: skill.name, path: skill.dir } });
+            else
+                console.log(skill.dir);
+            return;
+        }
+        case "help": {
+            showSkillsHelp();
+            return;
+        }
+        default:
+            throw new Error(`Unknown skills subcommand: ${subcommand}`);
+    }
+}
+function showSkillsHelp() {
+    console.log("Usage: qmd skills <list|get|path> [options]");
+    console.log("");
+    console.log("Commands:");
+    console.log("  list                 List bundled runtime skills");
+    console.log("  get <name>           Print a bundled runtime skill");
+    console.log("  get <name> --full    Include references/templates/scripts");
+    console.log("  get --all            Print all bundled runtime skills");
+    console.log("  path [name]          Print runtime skill directory path(s)");
+    console.log("");
+    console.log("Options:");
+    console.log("  --json               Print structured JSON");
+}
+function ensureClaudeSymlink(linkPath, targetDir, force) {
+    const parentDir = dirname(linkPath);
+    if (pathExists(parentDir)) {
+        const resolvedTargetDir = realpathSync(dirname(targetDir));
+        const resolvedLinkParent = realpathSync(parentDir);
+        // If .claude/skills already resolves to the same directory as .agents/skills,
+        // the skill is already visible to Claude and creating qmd -> qmd would loop.
+        if (resolvedTargetDir === resolvedLinkParent) {
+            return false;
+        }
+    }
+    const linkTarget = relativePath(parentDir, targetDir) || ".";
+    mkdirSync(parentDir, { recursive: true });
+    if (pathExists(linkPath)) {
+        const stat = lstatSync(linkPath);
+        if (stat.isSymbolicLink() && readlinkSync(linkPath) === linkTarget) {
+            return true;
+        }
+        if (!force) {
+            throw new Error(`Claude skill path already exists: ${linkPath} (use --force to replace it)`);
+        }
+        removePath(linkPath);
+    }
+    symlinkSync(linkTarget, linkPath, "dir");
+    return true;
+}
+async function shouldCreateClaudeSymlink(linkPath, autoYes) {
+    if (autoYes) {
+        return true;
+    }
+    if (!process.stdin.isTTY || !process.stdout.isTTY) {
+        console.log(`Tip: create a Claude symlink manually at ${linkPath}`);
+        return false;
+    }
+    const rl = createInterface({
+        input: process.stdin,
+        output: process.stdout,
+    });
+    try {
+        const answer = await rl.question(`Create a symlink in ${linkPath}? [y/N] `);
+        const normalized = answer.trim().toLowerCase();
+        return normalized === "y" || normalized === "yes";
+    }
+    finally {
+        rl.close();
+    }
+}
+async function installSkill(globalInstall, force, autoYes) {
+    const installDir = getSkillInstallDir(globalInstall);
+    writeSkillInstall(installDir, force);
+    console.log(`✓ Installed QMD skill to ${installDir}`);
+    const claudeLinkPath = getClaudeSkillLinkPath(globalInstall);
+    if (!(await shouldCreateClaudeSymlink(claudeLinkPath, autoYes))) {
+        return;
+    }
+    const linked = ensureClaudeSymlink(claudeLinkPath, installDir, force);
+    if (linked) {
+        console.log(`✓ Linked Claude skill at ${claudeLinkPath}`);
+    }
+    else {
+        console.log(`✓ Claude already sees the skill via ${dirname(claudeLinkPath)}`);
+    }
+}
+function showHelp() {
+    console.log("qmd — Quick Markdown Search");
+    console.log("");
+    console.log("Usage:");
+    console.log("  qmd <command> [options]");
+    console.log("");
+    console.log("Primary commands:");
+    console.log("  qmd query <query>             - Hybrid search with auto expansion + reranking (recommended)");
+    console.log("  qmd query 'lex:..\\nvec:...'   - Structured query document (you provide lex/vec/hyde lines)");
+    console.log("  qmd search <query>            - Full-text BM25 keywords (no LLM)");
+    console.log("  qmd vsearch <query>           - Vector similarity only");
+    console.log("  qmd get <file>[:from[:count]] - Show a document (line-numbered; #docid in header)");
+    console.log("  qmd multi-get <pattern>       - Batch fetch via glob or comma-separated list");
+    console.log("  qmd skills list/get/path      - List and retrieve bundled runtime skills");
+    console.log("  qmd skill show/install        - Show or install the QMD skill");
+    console.log("  qmd mcp                       - Start the MCP server (stdio transport for AI agents)");
+    console.log("  qmd bench <fixture.json>      - Run search quality benchmarks against a fixture file");
+    console.log("");
+    console.log("Collections & context:");
+    console.log("  qmd collection add/list/remove/rename/show   - Manage indexed folders");
+    console.log("  qmd context add/list/rm                      - Attach human-written summaries");
+    console.log("  qmd ls [collection[/path]]                   - Inspect indexed files");
+    console.log("");
+    console.log("Maintenance:");
+    console.log("  qmd init                      - Create a project-local .qmd index");
+    console.log("  qmd status                    - View index + collection health");
+    console.log("  qmd update [--pull]           - Re-index collections (optionally git pull first)");
+    console.log("  qmd embed [-f] [-c <name>]    - Generate/refresh vector embeddings");
+    console.log("    --max-docs-per-batch <n>    - Cap docs loaded into memory per embedding batch");
+    console.log("    --max-batch-mb <n>          - Cap UTF-8 MB loaded into memory per embedding batch");
+    console.log("  qmd cleanup                   - Clear caches, vacuum DB");
+    console.log("");
+    console.log("Query syntax (qmd query):");
+    console.log("  QMD queries are either a single expand query (no prefix) or a multi-line");
+    console.log("  document where every line is typed with lex:, vec:, or hyde:. This grammar");
+    console.log("  matches the docs in docs/SYNTAX.md and is enforced in the CLI.");
+    console.log("");
+    const grammar = [
+        `query          = expand_query | query_document ;`,
+        `expand_query   = text | explicit_expand ;`,
+        `explicit_expand= "expand:" text ;`,
+        `query_document = [ intent_line ] { typed_line } ;`,
+        `intent_line    = "intent:" text newline ;`,
+        `typed_line     = type ":" text newline ;`,
+        `type           = "lex" | "vec" | "hyde" ;`,
+        `text           = quoted_phrase | plain_text ;`,
+        `quoted_phrase  = '"' { character } '"' ;`,
+        `plain_text     = { character } ;`,
+        `newline        = "\\n" ;`,
+    ];
+    console.log("  Grammar:");
+    for (const line of grammar) {
+        console.log(`    ${line}`);
+    }
+    console.log("");
+    console.log("  Examples:");
+    console.log("    qmd query \"how does auth work\"                # single-line → implicit expand");
+    console.log("    qmd query $'lex: CAP theorem\\nvec: consistency'  # typed query document");
+    console.log("    qmd query $'lex: \"exact matches\" sports -baseball'  # phrase + negation lex search");
+    console.log("    qmd query $'hyde: Hypothetical answer text'       # hyde-only document");
+    console.log("");
+    console.log("  Constraints:");
+    console.log("    - Standalone expand queries cannot mix with typed lines.");
+    console.log("    - Query documents allow only lex:, vec:, or hyde: prefixes.");
+    console.log("    - Each typed line must be single-line text with balanced quotes.");
+    console.log("");
+    console.log("AI agents & integrations:");
+    console.log("  - Run `qmd mcp` to expose the MCP server (stdio) to agents/IDEs.");
+    console.log("  - Run `qmd skills get qmd --full` for version-matched agent instructions.");
+    console.log("  - `qmd skill install` installs the QMD skill into ./.agents/skills/qmd.");
+    console.log("  - Use `qmd skill install --global` for ~/.agents/skills/qmd.");
+    console.log("  - `qmd --skill` is kept as an alias for `qmd skill show`.");
+    console.log("  - Advanced: `qmd mcp --http ...` and `qmd mcp --http --daemon` are optional for custom transports.");
+    console.log("");
+    console.log("Global options:");
+    console.log("  --index <name>             - Use a named index (default: index)");
+    console.log("  QMD_EDITOR_URI             - Editor link template for clickable TTY search output");
+    console.log("");
+    console.log("Search options:");
+    console.log("  -n <num>                   - Max results (default 5, or 20 for --format files|json)");
+    console.log("  --all                      - Return all matches (pair with --min-score)");
+    console.log("  --min-score <num>          - Minimum similarity score");
+    console.log("  --full                     - Output full document instead of snippet");
+    console.log("  -C, --candidate-limit <n>  - Max candidates to rerank (default 40, lower = faster)");
+    console.log("  --no-rerank                - Skip LLM reranking (use RRF scores only, much faster on CPU)");
+    console.log("  --no-gpu                   - Force CPU mode for llama.cpp operations (same as QMD_FORCE_CPU=1)");
+    console.log("  --line-numbers             - Include line numbers (search; get/multi-get are on by default)");
+    console.log("  --no-line-numbers          - Disable line numbers for get/multi-get");
+    console.log("  --full-path                - Show on-disk paths instead of qmd:// + docid (get/multi-get/search/query)");
+    console.log("                                Paths are ./-prefixed when under $PWD, absolute otherwise");
+    console.log("  --explain                  - Include retrieval score traces (query, CLI/--format json)");
+    console.log("  --format <kind>            - Output format: cli (default) | json | csv | md | xml | files");
+    console.log("  -c, --collection <name>    - Filter by one or more collections");
+    console.log("");
+    console.log("Embed/query options:");
+    console.log("  --chunk-strategy <auto|regex> - Chunking mode (default: regex; auto uses AST for code files)");
+    console.log("");
+    console.log("Multi-get options:");
+    console.log("  -l <num>                   - Maximum lines per file");
+    console.log("  --max-bytes <num>          - Skip files larger than N bytes (default 10240)");
+    console.log("  --format <kind>            - Same formats as search");
+    console.log("");
+    console.log(`Index: ${getDbPath()}`);
+}
+function doctorCheck(label, ok, details) {
+    const mark = ok ? `${c.green}✓${c.reset}` : `${c.yellow}⚠${c.reset}`;
+    console.log(`${mark} ${label}: ${details}`);
+}
+function formatCount(n) {
+    return n.toLocaleString("en-US");
+}
+function shortModelName(model) {
+    if (model.startsWith("hf:")) {
+        return model.split("/").pop() || model;
+    }
+    return model.length > 56 ? `${model.slice(0, 53)}...` : model;
+}
+function normalizedDoctorNextSteps(steps) {
+    const unique = Array.from(new Set(steps));
+    const hasForceEmbed = unique.some(step => step.includes("qmd embed --force"));
+    if (!hasForceEmbed)
+        return unique;
+    return unique.filter(step => !step.includes("qmd embed") || step.startsWith("Run `qmd embed --force`"));
+}
+function shortHashSeq(hashSeq) {
+    const idx = hashSeq.lastIndexOf("_");
+    if (idx < 0)
+        return hashSeq.length > 18 ? `${hashSeq.slice(0, 18)}...` : hashSeq;
+    return `${hashSeq.slice(0, 12)}_${hashSeq.slice(idx + 1)}`;
+}
+function decodeStoredEmbedding(bytes) {
+    return new Float32Array(bytes.buffer.slice(bytes.byteOffset, bytes.byteOffset + bytes.byteLength));
+}
+function cosineDistance(a, b) {
+    if (a.length !== b.length || a.length === 0)
+        return Number.POSITIVE_INFINITY;
+    let dot = 0;
+    let normA = 0;
+    let normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        const av = a[i] ?? 0;
+        const bv = b[i] ?? 0;
+        dot += av * bv;
+        normA += av * av;
+        normB += bv * bv;
+    }
+    if (normA === 0 || normB === 0)
+        return Number.POSITIVE_INFINITY;
+    return 1 - (dot / (Math.sqrt(normA) * Math.sqrt(normB)));
+}
+function formatModelDiagnosticPath(path) {
+    return sanitizeDiagnosticMessage(path);
+}
+function findCachedModelInspection(model) {
+    const invalid = [];
+    if (model.startsWith("hf:")) {
+        const filename = model.split("/").pop();
+        if (!filename || !existsSync(DEFAULT_MODEL_CACHE_DIR))
+            return { path: null, invalid };
+        const entries = readdirSync(DEFAULT_MODEL_CACHE_DIR, { withFileTypes: true });
+        for (const entry of entries) {
+            if (!entry.isFile() || !entry.name.includes(filename))
+                continue;
+            const candidate = pathJoin(DEFAULT_MODEL_CACHE_DIR, entry.name);
+            const inspection = inspectGgufFile(candidate);
+            if (inspection.valid)
+                return { path: candidate, invalid };
+            invalid.push(`${formatModelDiagnosticPath(candidate)}: ${inspection.details}`);
+        }
+        return { path: null, invalid };
+    }
+    const inspection = inspectGgufFile(model);
+    if (inspection.valid)
+        return { path: model, invalid };
+    if (inspection.exists)
+        invalid.push(`${formatModelDiagnosticPath(model)}: ${inspection.details}`);
+    return { path: null, invalid };
+}
+function envValueForDisplay(value) {
+    const sanitized = sanitizeDiagnosticMessage(value);
+    return sanitized.length > 96 ? `${sanitized.slice(0, 93)}...` : sanitized;
+}
+function collectEnvironmentOverrides(activeModels, configModels = {}) {
+    const overrides = [];
+    const add = (name, consequence) => {
+        const raw = process.env[name]?.trim();
+        if (!raw)
+            return;
+        overrides.push({ name, value: envValueForDisplay(raw), consequence });
+    };
+    const addModel = (name, key, active) => {
+        const raw = process.env[name]?.trim();
+        if (!raw)
+            return;
+        const configured = configModels[key];
+        const consequence = configured && configured !== raw
+            ? `set but ignored because index models.${key} is configured as ${configured}`
+            : `sets the active ${key} model to ${active}; changes embedding/search semantics and may require \`qmd pull\` plus \`qmd embed\``;
+        overrides.push({ name, value: envValueForDisplay(raw), consequence });
+    };
+    add("INDEX_PATH", "overrides the SQLite index path; QMD reads/writes a different database");
+    add("QMD_CONFIG_DIR", "overrides the QMD config directory and takes precedence over XDG_CONFIG_HOME");
+    add("XDG_CONFIG_HOME", "moves QMD config to $XDG_CONFIG_HOME/qmd when QMD_CONFIG_DIR is not set");
+    add("XDG_CACHE_HOME", "moves the default index cache, model cache, and MCP daemon PID files");
+    addModel("QMD_EMBED_MODEL", "embed", activeModels.embed);
+    addModel("QMD_GENERATE_MODEL", "generate", activeModels.generate);
+    addModel("QMD_RERANK_MODEL", "rerank", activeModels.rerank);
+    add("QMD_FORCE_CPU", "forces llama.cpp to bypass GPU backends; embeddings/query will be slower but GPU crashes are avoided");
+    add("QMD_LLAMA_GPU", "selects llama.cpp GPU backend (metal/cuda/vulkan) or disables GPU when set to false/off/0");
+    add("QMD_DOCTOR_DEVICE_PROBE", "controls qmd doctor native device probing; 0/off skips GPU probing");
+    add("QMD_EMBED_PARALLELISM", "overrides embedding parallel context count; too high can exhaust RAM/VRAM");
+    add("QMD_EXPAND_CONTEXT_SIZE", "overrides query expansion context size; larger values use more memory");
+    add("QMD_RERANK_CONTEXT_SIZE", "overrides reranker context size; larger values use more memory");
+    add("QMD_EMBED_CONTEXT_SIZE", "overrides embed context size; larger values use more memory");
+    add("QMD_EDITOR_URI", "overrides clickable editor link template in terminal output");
+    add("QMD_SKILLS_DIR", "overrides where qmd skills are discovered from");
+    add("QMD_METAL_KEEP_RESIDENCY", "opts back into libggml-metal residency sets on darwin; restores ~0ms perf wins for long-lived processes but re-exposes the static-destructor backtrace dump at process exit (ggml-org/llama.cpp#22593)");
+    add("GGML_METAL_NO_RESIDENCY", "set automatically by the launcher on darwin to disable Metal residency sets (avoids ggml-org/llama.cpp#22593); override via QMD_METAL_KEEP_RESIDENCY=1");
+    add("NO_COLOR", "disables colored terminal output");
+    add("CI", "disables real LLM operations inside QMD's LlamaCpp wrapper");
+    add("HF_ENDPOINT", "changes Hugging Face download endpoint used when pulling models");
+    add("QMD_WRAPPER_CAPTURE", "test/debug hook for the qmd shell wrapper; should not be set in normal use");
+    add("WSL_DISTRO_NAME", "enables WSL path handling heuristics");
+    add("WSL_INTEROP", "enables WSL path handling heuristics");
+    return overrides;
+}
+function checkDoctorIndexConfig(nextSteps) {
+    try {
+        const config = loadConfig();
+        const collectionCount = Object.keys(config.collections ?? {}).length;
+        if (collectionCount === 0) {
+            doctorCheck("index config", false, "no collections configured. Next: `qmd collection add .`");
+            nextSteps.push("Run `qmd collection add . --name <name>` from the folder you want to index, or edit .qmd/index.yml manually.");
+        }
+        else {
+            doctorCheck("index config", true, `${formatCount(collectionCount)} ${collectionCount === 1 ? "collection" : "collections"} configured`);
+        }
+        return { config, valid: true };
+    }
+    catch (error) {
+        const message = error instanceof Error ? sanitizeDiagnosticMessage(error.message) : sanitizeDiagnosticMessage(String(error));
+        const configPath = getConfigPath();
+        doctorCheck("index config", false, `invalid index.yml at ${configPath}: ${message}. Next: fix the YAML and rerun \`qmd doctor\``);
+        nextSteps.push(`Fix invalid YAML in ${configPath}, then rerun \`qmd doctor\`.`);
+        return { config: null, valid: false };
+    }
+}
+function checkEnvironmentOverrides(activeModels, configModels = {}) {
+    const overrides = collectEnvironmentOverrides(activeModels, configModels);
+    if (overrides.length === 0) {
+        doctorCheck("environment overrides", true, "none");
+        return;
+    }
+    doctorCheck("environment overrides", false, `${overrides.length} set`);
+    for (const override of overrides) {
+        console.log(`  - ${override.name}=${override.value}: ${override.consequence}`);
+    }
+}
+function checkModelDefaults(activeModels, configModels = {}) {
+    const checks = [
+        { role: "embedding", key: "embed", active: activeModels.embed, configured: configModels.embed, defaultModel: DEFAULT_EMBED_MODEL, envName: "QMD_EMBED_MODEL", envValue: process.env.QMD_EMBED_MODEL },
+        { role: "generation", key: "generate", active: activeModels.generate, configured: configModels.generate, defaultModel: DEFAULT_QUERY_MODEL, envName: "QMD_GENERATE_MODEL", envValue: process.env.QMD_GENERATE_MODEL },
+        { role: "reranking", key: "rerank", active: activeModels.rerank, configured: configModels.rerank, defaultModel: DEFAULT_RERANK_MODEL, envName: "QMD_RERANK_MODEL", envValue: process.env.QMD_RERANK_MODEL },
+    ];
+    const notes = [];
+    for (const check of checks) {
+        const envValue = check.envValue?.trim();
+        if (envValue && check.active === envValue) {
+            notes.push(`${check.role}: env ${check.envName}=${check.active} (default ${check.defaultModel}; might be ok)`);
+        }
+        else if (check.configured && check.configured !== check.defaultModel) {
+            notes.push(`${check.role}: index ${check.configured} (default ${check.defaultModel}; might be ok)`);
+        }
+        else if (envValue && check.active !== envValue) {
+            notes.push(`${check.role}: ${check.envName} is set to ${envValue} but index config uses ${check.active}`);
+        }
+    }
+    if (notes.length === 0) {
+        doctorCheck("model defaults", true, "using QMD codebase defaults");
+        return;
+    }
+    doctorCheck("model defaults", false, `non-default model configuration: ${notes.join("; ")}`);
+}
+function checkModelCache(activeModels, nextSteps) {
+    const models = [
+        ["embedding", activeModels.embed],
+        ["generation", activeModels.generate],
+        ["reranking", activeModels.rerank],
+    ];
+    const unique = new Map();
+    for (const [role, model] of models) {
+        unique.set(model, [...(unique.get(model) ?? []), role]);
+    }
+    const missing = [];
+    const cached = [];
+    const invalid = [];
+    for (const [model, roles] of unique) {
+        const label = `${roles.join("+")}: ${model}`;
+        const inspection = findCachedModelInspection(model);
+        invalid.push(...inspection.invalid.map(detail => `${label} (${detail})`));
+        if (inspection.path) {
+            cached.push(label);
+        }
+        else {
+            missing.push(label);
+        }
+    }
+    if (missing.length === 0 && invalid.length === 0) {
+        doctorCheck("model cache", true, `${cached.length} active ${cached.length === 1 ? "model is" : "models are"} downloaded and valid GGUF`);
+        return;
+    }
+    const parts = [];
+    if (invalid.length > 0)
+        parts.push(`invalid ${invalid.length}: ${invalid.join("; ")}`);
+    if (missing.length > 0)
+        parts.push(`missing ${missing.length}/${unique.size}: ${missing.join("; ")}`);
+    const next = invalid.length > 0
+        ? "Next: run `qmd pull --refresh` (or remove the bad cached file)"
+        : "Next: run `qmd pull`";
+    doctorCheck("model cache", false, `${parts.join("; ")}. ${next}`);
+    if (invalid.length > 0) {
+        nextSteps.push("Run `qmd pull --refresh` to replace invalid cached model files, or delete the listed file and rerun `qmd pull`.");
+    }
+    else {
+        nextSteps.push("Run `qmd pull` to download missing embedding/generation/reranking models before `qmd embed` or `qmd query`.");
+    }
+}
+async function checkEmbeddingVectorSamples(db, model, fingerprint, sampleSize = 3) {
+    const activeDocs = db.prepare(`SELECT COUNT(*) AS count FROM documents WHERE active = 1`).get().count;
+    if (activeDocs === 0) {
+        return { ok: true, details: "no active documents indexed" };
+    }
+    const vecTableExists = db.prepare(`SELECT 1 FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
+    if (!vecTableExists) {
+        return { ok: false, details: "no vector table to test; please run qmd embed again" };
+    }
+    const samples = db.prepare(`
+    SELECT cv.hash, cv.seq, c.doc AS body, MIN(d.path) AS path
+    FROM content_vectors cv
+    JOIN documents d ON d.hash = cv.hash AND d.active = 1
+    JOIN content c ON c.hash = cv.hash
+    WHERE cv.model = ? AND cv.embed_fingerprint = ?
+    GROUP BY cv.hash, cv.seq, c.doc
+    ORDER BY random()
+    LIMIT ?
+  `).all(model, fingerprint, sampleSize);
+    if (samples.length === 0) {
+        return { ok: false, details: "no current embedded chunks to test; please run qmd embed again" };
+    }
+    const threshold = 0.0001;
+    const mismatches = [];
+    await withLLMSession(async (session) => {
+        for (const sample of samples) {
+            const hashSeq = `${sample.hash}_${sample.seq}`;
+            const chunks = await chunkDocumentByTokens(sample.body, undefined, undefined, undefined, sample.path, undefined, session.signal);
+            const chunk = chunks[sample.seq];
+            if (!chunk) {
+                mismatches.push(`${shortHashSeq(hashSeq)}: chunk no longer exists`);
+                continue;
+            }
+            const title = extractTitle(sample.body, sample.path);
+            const result = await session.embed(formatDocForEmbedding(chunk.text, title, model), { model });
+            if (!result) {
+                mismatches.push(`${shortHashSeq(hashSeq)}: embedding failed`);
+                continue;
+            }
+            const stored = db.prepare(`SELECT embedding FROM vectors_vec WHERE hash_seq = ?`).get(hashSeq);
+            if (!stored) {
+                mismatches.push(`${shortHashSeq(hashSeq)}: stored vector missing`);
+                continue;
+            }
+            const distance = cosineDistance(result.embedding, decodeStoredEmbedding(stored.embedding));
+            if (distance > threshold) {
+                mismatches.push(`${shortHashSeq(hashSeq)}: stored vector distance ${distance.toFixed(6)}`);
+            }
+        }
+    }, { maxDuration: 10 * 60 * 1000, name: "doctorEmbeddingVectorSample" });
+    if (mismatches.length > 0) {
+        return {
+            ok: false,
+            details: `${mismatches.length}/${samples.length} sampled chunks differ from stored vectors (${mismatches[0]}). Rebuild with \`qmd embed --force\``,
+        };
+    }
+    return {
+        ok: true,
+        details: `${samples.length} sampled ${samples.length === 1 ? "chunk" : "chunks"} reproduce stored vectors`,
+    };
+}
+function hasLibraryInDirs(libraryBaseName, dirs) {
+    for (const dir of dirs) {
+        if (!dir || !existsSync(dir))
+            continue;
+        try {
+            for (const entry of readdirSync(dir)) {
+                if (entry === libraryBaseName || entry.startsWith(`${libraryBaseName}.`))
+                    return true;
+            }
+        }
+        catch { /* ignore unreadable system library dirs */ }
+    }
+    return false;
+}
+function linuxCudaRuntimeDiagnostic() {
+    if (process.platform !== "linux")
+        return null;
+    const dirs = new Set();
+    for (const value of [process.env.LD_LIBRARY_PATH, process.env.CUDA_PATH]) {
+        for (const part of (value ?? "").split(":")) {
+            if (part)
+                dirs.add(part);
+        }
+    }
+    if (process.env.CUDA_PATH) {
+        dirs.add(pathJoin(process.env.CUDA_PATH, "lib64"));
+        dirs.add(pathJoin(process.env.CUDA_PATH, "targets", "x86_64-linux", "lib"));
+    }
+    for (const dir of ["/usr/lib", "/usr/lib64", "/usr/lib/x86_64-linux-gnu", "/usr/local/cuda/lib64", "/usr/local/cuda/targets/x86_64-linux/lib"]) {
+        dirs.add(dir);
+    }
+    try {
+        for (const entry of readdirSync("/usr/local")) {
+            if (!entry.toLowerCase().startsWith("cuda-"))
+                continue;
+            const cudaRoot = pathJoin("/usr/local", entry);
+            dirs.add(pathJoin(cudaRoot, "lib64"));
+            dirs.add(pathJoin(cudaRoot, "targets", "x86_64-linux", "lib"));
+        }
+    }
+    catch { /* /usr/local may not be readable in restricted environments */ }
+    const searchDirs = [...dirs];
+    const hasDriver = hasLibraryInDirs("libcuda.so", searchDirs) || hasLibraryInDirs("libnvidia-ml.so", searchDirs);
+    if (!hasDriver)
+        return null;
+    const cudaLibraries = [
+        ["libcudart.so", "CUDA runtime"],
+        ["libcublas.so", "cuBLAS"],
+        ["libcublasLt.so", "cuBLASLt"],
+    ];
+    const missing = cudaLibraries
+        .filter(([library]) => !hasLibraryInDirs(library, searchDirs))
+        .map(([, label]) => label);
+    if (missing.length === 0)
+        return null;
+    return `NVIDIA driver libraries are visible, but CUDA user-space libraries are missing from loader paths (${missing.join(", ")})`;
+}
+async function runDoctorDeviceChecks(nextSteps) {
+    const mode = configuredGpuModeLabel();
+    doctorCheck("device mode", true, mode);
+    const skipProbe = ["0", "false", "off", "no", "skip"].includes((process.env.QMD_DOCTOR_DEVICE_PROBE ?? "").trim().toLowerCase());
+    if (skipProbe) {
+        doctorCheck("device probe", false, "skipped by QMD_DOCTOR_DEVICE_PROBE=0. Next: unset it and rerun `qmd doctor` to verify GPU/CPU acceleration");
+        nextSteps.push("Unset `QMD_DOCTOR_DEVICE_PROBE` and rerun `qmd doctor` when you want to verify llama.cpp device acceleration.");
+        return;
+    }
+    const crashHint = "Probing native llama backend now. If qmd crashes here, rerun with `QMD_FORCE_CPU=1 qmd doctor` (or `QMD_DOCTOR_DEVICE_PROBE=0 qmd doctor` to skip this probe).";
+    if (process.stdout.isTTY) {
+        process.stdout.write(`${c.dim}${crashHint}${c.reset}`);
+    }
+    try {
+        const device = await getDefaultLlamaCpp().getDeviceInfo({ allowBuild: false });
+        if (process.stdout.isTTY) {
+            process.stdout.write(`\r${" ".repeat(crashHint.length)}\r`);
+        }
+        if (device.gpu) {
+            const gpuLabel = device.gpu === "metal" && process.platform === "darwin"
+                ? "metal (macOS Metal backend)"
+                : String(device.gpu);
+            const parts = [`GPU ${gpuLabel}`, `offloading ${device.gpuOffloading ? "enabled" : "disabled"}`];
+            if (device.gpuDevices.length > 0)
+                parts.push(`devices: ${summarizeDeviceNames(device.gpuDevices)}`);
+            if (device.vram)
+                parts.push(`VRAM ${formatBytes(device.vram.free)} free / ${formatBytes(device.vram.total)} total`);
+            parts.push(`${device.cpuCores} CPU math cores`);
+            doctorCheck("device probe", device.gpuOffloading, device.gpuOffloading
+                ? parts.join("; ")
+                : `${parts.join("; ")}. Next: check QMD_LLAMA_GPU and llama.cpp backend support`);
+            if (!device.gpuOffloading) {
+                nextSteps.push("GPU was detected but offloading is disabled; check `QMD_LLAMA_GPU=metal|cuda|vulkan` and rerun `qmd doctor`.");
+            }
+            // Surface the darwin residency-set mitigation. libggml-metal's
+            // process-static device dtor asserts on un-expired residency sets
+            // during libc exit() (ggml-org/llama.cpp#22593), producing a giant
+            // stderr backtrace after correct output. The bin/qmd launcher exports
+            // GGML_METAL_NO_RESIDENCY=1 on darwin to skip the assertion entirely.
+            // No measurable perf cost on short-lived CLI calls.
+            if (device.gpu === "metal" && process.platform === "darwin") {
+                if (isDarwinMetalMitigationActive()) {
+                    doctorCheck("darwin metal residency", true, "GGML_METAL_NO_RESIDENCY=1 set by launcher; clean process exit (avoids ggml-org/llama.cpp#22593). Opt back in with QMD_METAL_KEEP_RESIDENCY=1 if you run long-lived qmd processes.");
+                }
+                else {
+                    doctorCheck("darwin metal residency", false, "residency sets active (QMD_METAL_KEEP_RESIDENCY=1 or launcher bypassed); llama-using commands may dump a libggml-metal backtrace at exit (ggml-org/llama.cpp#22593) even when output succeeded.");
+                    nextSteps.push("Unset `QMD_METAL_KEEP_RESIDENCY` so the launcher can disable Metal residency sets; without this, query/vsearch/embed dump a stack trace at exit even on success.");
+                }
+            }
+        }
+        else {
+            const cudaDiagnostic = linuxCudaRuntimeDiagnostic();
+            const diagnosticSuffix = cudaDiagnostic ? ` ${cudaDiagnostic}.` : "";
+            doctorCheck("device probe", false, `running on CPU (${device.cpuCores} math cores).${diagnosticSuffix} Next: install/configure Metal, CUDA, or Vulkan for faster embeddings, or set QMD_FORCE_CPU=1 to make CPU mode explicit`);
+            if (cudaDiagnostic) {
+                nextSteps.push(`${cudaDiagnostic}; install CUDA runtime/cuBLAS libraries or add their directory to LD_LIBRARY_PATH, then rerun \`qmd doctor\`.`);
+            }
+            else {
+                nextSteps.push("Vector operations are running on CPU; install/configure Metal, CUDA, or Vulkan if embedding/query performance is too slow.");
+            }
+        }
+    }
+    catch (error) {
+        if (process.stdout.isTTY) {
+            process.stdout.write(`\r${" ".repeat(crashHint.length)}\r`);
+        }
+        const message = error instanceof Error ? sanitizeDiagnosticMessage(error.message) : sanitizeDiagnosticMessage(String(error));
+        doctorCheck("device probe", false, `probe failed: ${message}. Next: run with QMD_FORCE_CPU=1 to bypass GPU probing, or set QMD_LLAMA_GPU=metal|cuda|vulkan and retry`);
+        nextSteps.push("GPU probe failed; try `QMD_FORCE_CPU=1 qmd doctor` to confirm CPU fallback, then fix GPU drivers/backend if acceleration is expected.");
+    }
+}
+async function showDoctor() {
+    const storeInstance = getStore();
+    const db = storeInstance.db;
+    const pkg = readPackageJson();
+    const activeModels = resolveModelsForCli();
+    const embedModel = activeModels.embed;
+    const fingerprint = getEmbeddingFingerprint(embedModel);
+    const nextSteps = [];
+    console.log(`${c.bold}QMD Doctor${c.reset}\n`);
+    console.log(`Index: ${getDbPath()}`);
+    console.log(`Runtime: ${isBun ? "bun:sqlite" : "better-sqlite3"}`);
+    try {
+        const row = db.prepare(`SELECT sqlite_version() AS version`).get();
+        doctorCheck("SQLite runtime", true, row.version);
+    }
+    catch (error) {
+        doctorCheck("SQLite runtime", false, error instanceof Error ? error.message : String(error));
+    }
+    const betterSqliteVersion = pkg.dependencies?.["better-sqlite3"] ?? pkg.devDependencies?.["better-sqlite3"] ?? "not declared";
+    doctorCheck("better-sqlite3 package", true, String(betterSqliteVersion));
+    try {
+        const row = db.prepare(`SELECT vec_version() AS version`).get();
+        doctorCheck("sqlite-vec", true, row.version);
+    }
+    catch (error) {
+        doctorCheck("sqlite-vec", false, error instanceof Error ? error.message : String(error));
+    }
+    // CJK tokenizer check (qmd-ja: Vaporetto WASM)
+    try {
+        await initializeVaporettoTokenizer();
+        const modelPath = resolveVaporettoModelPath();
+        const modelName = modelPath.split("/").pop() ?? modelPath;
+        let ftsLabel = "not indexed yet";
+        try {
+            const row = db.prepare(`SELECT value FROM store_config WHERE key = 'fts_cjk_normalized_version'`).get();
+            if (row?.value === FTS_CJK_NORMALIZED_VERSION) {
+                ftsLabel = `v${FTS_CJK_NORMALIZED_VERSION} (current)`;
+            }
+            else if (row?.value) {
+                ftsLabel = `v${row.value} -> v${FTS_CJK_NORMALIZED_VERSION} (stale, run qmd-ja update)`;
+            }
+        }
+        catch { /* ignore */ }
+        doctorCheck("CJK tokenizer", true, `Vaporetto WASM — model: ${modelName}, FTS index: ${ftsLabel}`);
+    }
+    catch (error) {
+        doctorCheck("CJK tokenizer", false, `Vaporetto WASM failed: ${error instanceof Error ? error.message : String(error)}`);
+    }
+    const configCheck = checkDoctorIndexConfig(nextSteps);
+    const configModels = configCheck.config?.models ?? {};
+    checkEnvironmentOverrides(activeModels, configModels);
+    checkModelDefaults(activeModels, configModels);
+    checkModelCache(activeModels, nextSteps);
+    await runDoctorDeviceChecks(nextSteps);
+    try {
+        const adoption = await maybeAdoptLegacyEmbeddingFingerprint(storeInstance, embedModel);
+        if (adoption.checked || adoption.adopted > 0) {
+            doctorCheck("legacy fingerprint adoption", adoption.adopted > 0, adoption.adopted > 0 ? `adopted ${adoption.adopted} legacy chunks; ${adoption.reason}` : adoption.reason);
+        }
+    }
+    catch (error) {
+        doctorCheck("legacy fingerprint adoption", false, error instanceof Error ? error.message : String(error));
+    }
+    try {
+        const pending = getHashesNeedingEmbedding(db, undefined, embedModel);
+        doctorCheck("embedding freshness", pending === 0, pending === 0 ? "all active documents match current fingerprint" : `${formatCount(pending)} active documents need embeddings. Next: \`qmd embed\``);
+        if (pending > 0) {
+            nextSteps.push(`Run \`qmd embed\` to generate ${formatCount(pending)} missing/stale document embeddings.`);
+        }
+    }
+    catch (error) {
+        doctorCheck("embedding freshness", false, error instanceof Error ? error.message : String(error));
+    }
+    try {
+        const rows = db.prepare(`
+      SELECT model, embed_fingerprint AS fingerprint, COUNT(DISTINCT hash) AS docs, COUNT(*) AS chunks
+      FROM content_vectors
+      GROUP BY model, embed_fingerprint
+      ORDER BY chunks DESC, model, embed_fingerprint
+    `).all();
+        const uniqueFingerprints = new Set(rows.map(row => row.fingerprint));
+        const offCurrent = rows.filter(row => row.model === embedModel && row.fingerprint !== fingerprint);
+        const ok = rows.length === 0 || (uniqueFingerprints.size === 1 && rows[0]?.fingerprint === fingerprint && offCurrent.length === 0);
+        const currentDocs = rows
+            .filter(row => row.model === embedModel && row.fingerprint === fingerprint)
+            .reduce((sum, row) => sum + row.docs, 0);
+        const otherDocs = rows.reduce((sum, row) => sum + row.docs, 0) - currentDocs;
+        const groups = rows.map(row => {
+            const label = row.fingerprint === fingerprint ? "current" : (row.fingerprint || "legacy");
+            return `${shortModelName(row.model)}:${label} ${formatCount(row.docs)} docs/${formatCount(row.chunks)} chunks`;
+        }).join("; ");
+        const namedFingerprintRows = rows.filter(row => row.fingerprint);
+        const namedFingerprints = [...new Set(namedFingerprintRows.map(row => row.fingerprint))];
+        if (namedFingerprints.length > 1) {
+            const namedGroups = namedFingerprintRows
+                .map(row => `${row.fingerprint}${row.fingerprint === fingerprint ? " (current)" : ""}: ${shortModelName(row.model)} ${formatCount(row.docs)} docs/${formatCount(row.chunks)} chunks`)
+                .join("; ");
+            doctorCheck("mixed named embedding fingerprints", false, `content_vectors contains ${namedFingerprints.length} named fingerprints: ${namedGroups}. Next: \`qmd embed\` or \`qmd embed --force\``);
+            nextSteps.push("Run `qmd embed` to converge mixed named embedding fingerprints; use `qmd embed --force` if old named fingerprints or vector sample mismatches remain.");
+        }
+        const details = rows.length === 0
+            ? `no vectors yet; current fingerprint ${fingerprint}`
+            : ok
+                ? `${formatCount(currentDocs)} docs on current fingerprint (${fingerprint})`
+                : `${formatCount(currentDocs)} docs current, ${formatCount(otherDocs)} docs legacy/stale. ${groups}. Next: \`qmd embed\``;
+        doctorCheck("embedding fingerprints", ok, details);
+        if (!ok) {
+            nextSteps.push("Run `qmd embed` to migrate active documents to the current embedding fingerprint; use `qmd embed --force` if vector samples still fail afterward.");
+        }
+    }
+    catch (error) {
+        doctorCheck("embedding fingerprints", false, error instanceof Error ? error.message : String(error));
+    }
+    try {
+        const vectorSample = await checkEmbeddingVectorSamples(db, embedModel, fingerprint);
+        doctorCheck("embedding vector sample", vectorSample.ok, vectorSample.details);
+        if (!vectorSample.ok) {
+            nextSteps.push("Run `qmd embed --force` to rebuild existing vectors that no longer reproduce under the current embedding pipeline.");
+        }
+    }
+    catch (error) {
+        const message = error instanceof Error ? sanitizeDiagnosticMessage(error.message) : sanitizeDiagnosticMessage(String(error));
+        doctorCheck("embedding vector sample", false, `${message}; rebuild with \`qmd embed --force\``);
+        nextSteps.push("Run `qmd embed --force` to rebuild existing vectors, then rerun `qmd doctor`.");
+    }
+    const steps = normalizedDoctorNextSteps(nextSteps);
+    if (steps.length > 0) {
+        console.log(`\n${c.bold}Recommended next step${steps.length === 1 ? "" : "s"}${c.reset}`);
+        for (const step of steps) {
+            console.log(`  - ${step}`);
+        }
+    }
+    closeDb();
+}
+function printDoctorHint() {
+    console.error("If qmd still behaves unexpectedly, run 'qmd doctor' for diagnostics.");
+}
+function exitWithError(error, code = 1) {
+    console.error(error instanceof Error ? error.message : String(error));
+    printDoctorHint();
+    process.exit(code);
+}
+function readPackageJson() {
+    const scriptDir = dirname(fileURLToPath(import.meta.url));
+    const pkgPath = resolve(scriptDir, "..", "..", "package.json");
+    return JSON.parse(readFileSync(pkgPath, "utf-8"));
+}
+async function showVersion() {
+    const scriptDir = dirname(fileURLToPath(import.meta.url));
+    const pkg = readPackageJson();
+    let commit = "";
+    try {
+        commit = execSync(`git -C ${scriptDir} rev-parse --short HEAD`, { encoding: "utf-8", stdio: ["pipe", "pipe", "pipe"] }).trim();
+    }
+    catch {
+        // Not a git repo or git not available
+    }
+    const versionStr = commit ? `${pkg.version} (${commit})` : pkg.version;
+    console.log(`qmd-ja ${versionStr}`);
+}
+// Main CLI - only run if this is the main module
+const __filename = fileURLToPath(import.meta.url);
+const argv1 = process.argv[1];
+const isMain = argv1 === __filename
+    || argv1?.endsWith("/qmd.ts")
+    || argv1?.endsWith("/qmd.js")
+    || (argv1 != null && realpathSync(argv1) === __filename);
+if (isMain) {
+    // Flip to production mode only when this module is executed as the CLI
+    // entrypoint, not when imported for its exports. Tests must set INDEX_PATH
+    // or use createStore() with an explicit path.
+    enableProductionMode();
+    const cli = parseCLI();
+    if (cli.values.version) {
+        await showVersion();
+        process.exit(0);
+    }
+    if (cli.values.skill) {
+        showSkill();
+        process.exit(0);
+    }
+    if (cli.values.help && cli.command === "skill") {
+        console.log("Usage: qmd skill <show|install> [options]");
+        console.log("");
+        console.log("Commands:");
+        console.log("  show                 Print the QMD skill");
+        console.log("  install              Install QMD skill into ./.agents/skills/qmd");
+        console.log("");
+        console.log("Options:");
+        console.log("  --global             Install into ~/.agents/skills/qmd");
+        console.log("  --yes                Also create the .claude/skills/qmd symlink");
+        console.log("  -f, --force          Replace existing install or symlink");
+        process.exit(0);
+    }
+    if (!cli.command || cli.values.help) {
+        showHelp();
+        process.exit(cli.values.help ? 0 : 1);
+    }
+    switch (cli.command) {
+        case "context": {
+            const subcommand = cli.args[0];
+            if (!subcommand) {
+                console.error("Usage: qmd context <add|list|rm>");
+                console.error("");
+                console.error("Commands:");
+                console.error("  qmd context add [path] \"text\"  - Add context (defaults to current dir)");
+                console.error("  qmd context add / \"text\"       - Add global context to all collections");
+                console.error("  qmd context list                - List all contexts");
+                console.error("  qmd context rm <path>           - Remove context");
+                process.exit(1);
+            }
+            switch (subcommand) {
+                case "add": {
+                    if (cli.args.length < 2) {
+                        console.error("Usage: qmd context add [path] \"text\"");
+                        console.error("");
+                        console.error("Examples:");
+                        console.error("  qmd context add \"Context for current directory\"");
+                        console.error("  qmd context add . \"Context for current directory\"");
+                        console.error("  qmd context add /subfolder \"Context for subfolder\"");
+                        console.error("  qmd context add / \"Global context for all collections\"");
+                        console.error("");
+                        console.error("  Using virtual paths:");
+                        console.error("  qmd context add qmd://journals/ \"Context for entire journals collection\"");
+                        console.error("  qmd context add qmd://journals/2024 \"Context for 2024 journals\"");
+                        process.exit(1);
+                    }
+                    let pathArg;
+                    let contextText;
+                    // Check if first arg looks like a path or if it's the context text
+                    const firstArg = cli.args[1] || '';
+                    const secondArg = cli.args[2];
+                    if (secondArg) {
+                        // Two args: path + context
+                        pathArg = firstArg;
+                        contextText = cli.args.slice(2).join(" ");
+                    }
+                    else {
+                        // One arg: context only (use current directory)
+                        pathArg = undefined;
+                        contextText = firstArg;
+                    }
+                    await contextAdd(pathArg, contextText);
+                    break;
+                }
+                case "list": {
+                    contextList();
+                    break;
+                }
+                case "rm":
+                case "remove": {
+                    if (cli.args.length < 2 || !cli.args[1]) {
+                        console.error("Usage: qmd context rm <path>");
+                        console.error("Examples:");
+                        console.error("  qmd context rm /");
+                        console.error("  qmd context rm qmd://journals/2024");
+                        process.exit(1);
+                    }
+                    contextRemove(cli.args[1]);
+                    break;
+                }
+                default:
+                    console.error(`Unknown subcommand: ${subcommand}`);
+                    console.error("Available: add, list, rm");
+                    process.exit(1);
+            }
+            break;
+        }
+        case "get": {
+            if (!cli.args[0]) {
+                console.error("Usage: qmd get <filepath>[:from[:count]] [--from <line>] [-l <lines>] [--no-line-numbers] [--full-path]");
+                process.exit(1);
+            }
+            const fromLine = cli.values.from ? parseInt(cli.values.from, 10) : undefined;
+            const maxLines = cli.values.l ? parseInt(cli.values.l, 10) : undefined;
+            // Line numbers default ON for get; opt out with --no-line-numbers.
+            const getLineNumbers = !cli.values["no-line-numbers"];
+            getDocument(cli.args[0], fromLine, maxLines, getLineNumbers, !!cli.values["full-path"]);
+            break;
+        }
+        case "multi-get": {
+            if (!cli.args[0]) {
+                console.error("Usage: qmd multi-get <pattern> [-l <lines>] [--max-bytes <bytes>] [--no-line-numbers] [--full-path] [--format json|csv|md|xml|files]");
+                console.error("  pattern: glob (e.g., 'journals/2025-05*.md') or comma-separated list");
+                process.exit(1);
+            }
+            const maxLinesMulti = cli.values.l ? parseInt(cli.values.l, 10) : undefined;
+            const maxBytes = cli.values["max-bytes"] ? parseInt(cli.values["max-bytes"], 10) : DEFAULT_MULTI_GET_MAX_BYTES;
+            // Line numbers default ON for multi-get; opt out with --no-line-numbers.
+            const mgLineNumbers = !cli.values["no-line-numbers"];
+            multiGet(cli.args[0], maxLinesMulti, maxBytes, cli.opts.format, mgLineNumbers, !!cli.values["full-path"]);
+            break;
+        }
+        case "ls": {
+            listFiles(cli.args[0]);
+            break;
+        }
+        case "collection": {
+            const subcommand = cli.args[0];
+            switch (subcommand) {
+                case "list": {
+                    collectionList();
+                    break;
+                }
+                case "add": {
+                    const pwd = cli.args[1] || getPwd();
+                    const resolvedPwd = pwd === '.' ? getPwd() : getRealPath(resolve(pwd));
+                    const globPattern = cli.values.mask || DEFAULT_GLOB;
+                    const name = cli.values.name;
+                    await collectionAdd(resolvedPwd, globPattern, name);
+                    break;
+                }
+                case "remove":
+                case "rm": {
+                    if (!cli.args[1]) {
+                        console.error("Usage: qmd collection remove <name>");
+                        console.error("  Use 'qmd collection list' to see available collections");
+                        process.exit(1);
+                    }
+                    collectionRemove(cli.args[1]);
+                    break;
+                }
+                case "rename":
+                case "mv": {
+                    if (!cli.args[1] || !cli.args[2]) {
+                        console.error("Usage: qmd collection rename <old-name> <new-name>");
+                        console.error("  Use 'qmd collection list' to see available collections");
+                        process.exit(1);
+                    }
+                    collectionRename(cli.args[1], cli.args[2]);
+                    break;
+                }
+                case "set-update":
+                case "update-cmd": {
+                    const name = cli.args[1];
+                    const cmd = cli.args.slice(2).join(' ') || null;
+                    if (!name) {
+                        console.error("Usage: qmd collection update-cmd <name> [command]");
+                        console.error("  Set the command to run before indexing (e.g., 'git pull')");
+                        console.error("  Omit command to clear it");
+                        process.exit(1);
+                    }
+                    const { updateCollectionSettings, getCollection } = await import("../collections.js");
+                    const col = getCollection(name);
+                    if (!col) {
+                        console.error(`Collection not found: ${name}`);
+                        process.exit(1);
+                    }
+                    updateCollectionSettings(name, { update: cmd });
+                    if (cmd) {
+                        console.log(`✓ Set update command for '${name}': ${cmd}`);
+                    }
+                    else {
+                        console.log(`✓ Cleared update command for '${name}'`);
+                    }
+                    break;
+                }
+                case "include":
+                case "exclude": {
+                    const name = cli.args[1];
+                    if (!name) {
+                        console.error(`Usage: qmd collection ${subcommand} <name>`);
+                        console.error(`  ${subcommand === 'include' ? 'Include' : 'Exclude'} collection in default queries`);
+                        process.exit(1);
+                    }
+                    const { updateCollectionSettings, getCollection } = await import("../collections.js");
+                    const col = getCollection(name);
+                    if (!col) {
+                        console.error(`Collection not found: ${name}`);
+                        process.exit(1);
+                    }
+                    const include = subcommand === 'include';
+                    updateCollectionSettings(name, { includeByDefault: include });
+                    console.log(`✓ Collection '${name}' ${include ? 'included in' : 'excluded from'} default queries`);
+                    break;
+                }
+                case "show":
+                case "info": {
+                    const name = cli.args[1];
+                    if (!name) {
+                        console.error("Usage: qmd collection show <name>");
+                        process.exit(1);
+                    }
+                    const { getCollection } = await import("../collections.js");
+                    const col = getCollection(name);
+                    if (!col) {
+                        console.error(`Collection not found: ${name}`);
+                        process.exit(1);
+                    }
+                    console.log(`Collection: ${name}`);
+                    console.log(`  Path:     ${col.path}`);
+                    console.log(`  Pattern:  ${col.pattern}`);
+                    console.log(`  Include:  ${col.includeByDefault !== false ? 'yes (default)' : 'no'}`);
+                    if (col.update) {
+                        console.log(`  Update:   ${col.update}`);
+                    }
+                    if (col.context) {
+                        const ctxCount = Object.keys(col.context).length;
+                        console.log(`  Contexts: ${ctxCount}`);
+                    }
+                    break;
+                }
+                case "help":
+                case undefined: {
+                    console.log("Usage: qmd collection <command> [options]");
+                    console.log("");
+                    console.log("Commands:");
+                    console.log("  list                      List all collections");
+                    console.log("  add <path> [--name NAME]  Add a collection");
+                    console.log("  remove <name>             Remove a collection");
+                    console.log("  rename <old> <new>        Rename a collection");
+                    console.log("  show <name>               Show collection details");
+                    console.log("  update-cmd <name> [cmd]   Set pre-update command (e.g., 'git pull')");
+                    console.log("  include <name>            Include in default queries");
+                    console.log("  exclude <name>            Exclude from default queries");
+                    console.log("");
+                    console.log("Examples:");
+                    console.log("  qmd collection add ~/notes --name notes");
+                    console.log("  qmd collection update-cmd brain 'git pull'");
+                    console.log("  qmd collection exclude archive");
+                    process.exit(0);
+                }
+                default:
+                    console.error(`Unknown subcommand: ${subcommand}`);
+                    console.error("Run 'qmd collection help' for usage");
+                    printDoctorHint();
+                    process.exit(1);
+            }
+            break;
+        }
+        case "init":
+            try {
+                initLocalIndex();
+            }
+            catch (error) {
+                exitWithError(error);
+            }
+            break;
+        case "status":
+            await showStatus();
+            break;
+        case "doctor":
+            await showDoctor();
+            break;
+        case "update":
+            await updateCollections();
+            break;
+        case "embed":
+            try {
+                const maxDocsPerBatch = parseEmbedBatchOption("maxDocsPerBatch", cli.values["max-docs-per-batch"]);
+                const maxBatchMb = parseEmbedBatchOption("maxBatchBytes", cli.values["max-batch-mb"]);
+                const embedChunkStrategy = parseChunkStrategy(cli.values["chunk-strategy"]);
+                // Validate -c against configured collections before dispatching, so a
+                // typo errors with "Collection not found: X" instead of silently
+                // reporting success because no pending docs match a nonexistent name.
+                // embed operates on a single collection; only the first value is used.
+                const embedValidatedCollections = resolveCollectionFilter(cli.opts.collection, false);
+                const embedCollection = embedValidatedCollections[0];
+                await vectorIndex(resolveEmbedModelForCli(), !!cli.values.force, {
+                    maxDocsPerBatch,
+                    maxBatchBytes: maxBatchMb === undefined ? undefined : maxBatchMb * 1024 * 1024,
+                    chunkStrategy: embedChunkStrategy,
+                    collection: embedCollection,
+                });
+            }
+            catch (error) {
+                exitWithError(error);
+            }
+            break;
+        case "pull": {
+            const refresh = cli.values.refresh === undefined ? false : Boolean(cli.values.refresh);
+            const activeModels = resolveModelsForCli();
+            const models = [
+                activeModels.embed,
+                activeModels.generate,
+                activeModels.rerank,
+            ];
+            console.log(`${c.bold}Pulling models${c.reset}`);
+            const results = await pullModels(models, {
+                refresh,
+                cacheDir: DEFAULT_MODEL_CACHE_DIR,
+            });
+            for (const result of results) {
+                const size = formatBytes(result.sizeBytes);
+                const note = result.refreshed ? "refreshed" : "cached/checked";
+                console.log(`- ${result.model} -> ${result.path} (${size}, ${note})`);
+            }
+            break;
+        }
+        case "search":
+            if (!cli.query) {
+                console.error("Usage: qmd search [options] <query>");
+                process.exit(1);
+            }
+            await initializeKuromojiTokenizer(); // kuromoji: normalize CJK query
+            search(cli.query, cli.opts);
+            break;
+        case "vsearch":
+        case "vector-search": // undocumented alias
+            if (!cli.query) {
+                console.error("Usage: qmd vsearch [options] <query>");
+                process.exit(1);
+            }
+            // Default min-score for vector search is 0.3
+            if (!cli.values["min-score"]) {
+                cli.opts.minScore = 0.3;
+            }
+            await vectorSearch(cli.query, cli.opts);
+            break;
+        case "query":
+        case "deep-search": // undocumented alias
+            if (!cli.query) {
+                console.error("Usage: qmd query [options] <query>");
+                process.exit(1);
+            }
+            await initializeKuromojiTokenizer(); // kuromoji: normalize CJK query
+            await querySearch(cli.query, cli.opts);
+            break;
+        case "bench": {
+            const fixturePath = cli.args[0];
+            if (!fixturePath) {
+                console.error("Usage: qmd bench <fixture.json> [--json] [-c collection]");
+                console.error("");
+                console.error("Run search quality benchmarks against a fixture file.");
+                console.error("See src/bench/fixtures/example.json for the fixture format.");
+                process.exit(1);
+            }
+            const { runBenchmark } = await import("../bench/bench.js");
+            const benchCollection = cli.opts.collection;
+            await runBenchmark(fixturePath, {
+                json: !!cli.values.json,
+                collection: Array.isArray(benchCollection) ? benchCollection[0] : benchCollection,
+                dbPath: getDbPath(),
+                configPath: configExists() ? getConfigPath() : undefined,
+            });
+            break;
+        }
+        case "mcp": {
+            const sub = cli.args[0]; // stop | status | undefined
+            // Cache dir for PID/log files — same dir as the index
+            const cacheDir = process.env.XDG_CACHE_HOME
+                ? resolve(process.env.XDG_CACHE_HOME, "qmd")
+                : resolve(homedir(), ".cache", "qmd");
+            const pidPath = resolve(cacheDir, "mcp.pid");
+            // Subcommands take priority over flags
+            if (sub === "stop") {
+                if (!existsSync(pidPath)) {
+                    console.log("Not running (no PID file).");
+                    process.exit(0);
+                }
+                const pid = parseInt(readFileSync(pidPath, "utf-8").trim());
+                try {
+                    process.kill(pid, 0); // alive?
+                    process.kill(pid, "SIGTERM");
+                    unlinkSync(pidPath);
+                    console.log(`Stopped QMD MCP server (PID ${pid}).`);
+                }
+                catch {
+                    unlinkSync(pidPath);
+                    console.log("Cleaned up stale PID file (server was not running).");
+                }
+                process.exit(0);
+            }
+            if (cli.values.http) {
+                const port = Number(cli.values.port) || 8181;
+                if (cli.values.daemon) {
+                    // Guard: check if already running
+                    if (existsSync(pidPath)) {
+                        const existingPid = parseInt(readFileSync(pidPath, "utf-8").trim());
+                        try {
+                            process.kill(existingPid, 0); // alive?
+                            console.error(`Already running (PID ${existingPid}). Run 'qmd mcp stop' first.`);
+                            process.exit(1);
+                        }
+                        catch {
+                            // Stale PID file — continue
+                        }
+                    }
+                    mkdirSync(cacheDir, { recursive: true });
+                    const logPath = resolve(cacheDir, "mcp.log");
+                    const logFd = openSync(logPath, "w"); // truncate — fresh log per daemon run
+                    const selfPath = fileURLToPath(import.meta.url);
+                    const indexArgs = cli.values.index ? ["--index", String(cli.values.index)] : [];
+                    const spawnArgs = selfPath.endsWith(".ts")
+                        ? ["--import", pathJoin(dirname(selfPath), "..", "..", "node_modules", "tsx", "dist", "esm", "index.mjs"), selfPath, ...indexArgs, "mcp", "--http", "--port", String(port)]
+                        : [selfPath, ...indexArgs, "mcp", "--http", "--port", String(port)];
+                    const child = nodeSpawn(process.execPath, spawnArgs, {
+                        stdio: ["ignore", logFd, logFd],
+                        detached: true,
+                    });
+                    child.unref();
+                    closeSync(logFd); // parent's copy; child inherited the fd
+                    writeFileSync(pidPath, String(child.pid));
+                    console.log(`Started on http://localhost:${port}/mcp (PID ${child.pid})`);
+                    console.log(`Logs: ${logPath}`);
+                    process.exit(0);
+                }
+                // Foreground HTTP mode — remove top-level cursor handlers so the
+                // async cleanup handlers in startMcpHttpServer actually run.
+                process.removeAllListeners("SIGTERM");
+                process.removeAllListeners("SIGINT");
+                const { startMcpHttpServer } = await import("../mcp/server.js");
+                try {
+                    await startMcpHttpServer(port, { dbPath: getDbPath() });
+                }
+                catch (e) {
+                    if (typeof e === "object" && e !== null && "code" in e && e.code === "EADDRINUSE") {
+                        console.error(`Port ${port} already in use. Try a different port with --port.`);
+                        process.exit(1);
+                    }
+                    throw e;
+                }
+            }
+            else {
+                // Default: stdio transport
+                const { startMcpServer } = await import("../mcp/server.js");
+                await startMcpServer({ dbPath: getDbPath() });
+            }
+            break;
+        }
+        case "skills": {
+            try {
+                if (cli.values.help || cli.args[0] === "help") {
+                    showSkillsHelp();
+                }
+                else {
+                    runSkillsCommand(cli.args, Boolean(cli.values.json), Boolean(cli.values.full), Boolean(cli.values.all));
+                }
+            }
+            catch (error) {
+                if (cli.values.json) {
+                    outputSkillsJson({ success: false, error: error instanceof Error ? error.message : String(error) });
+                }
+                else {
+                    console.error(error instanceof Error ? error.message : String(error));
+                }
+                process.exit(1);
+            }
+            break;
+        }
+        case "skill": {
+            const subcommand = cli.args[0];
+            switch (subcommand) {
+                case "show": {
+                    showSkill();
+                    break;
+                }
+                case "install": {
+                    try {
+                        await installSkill(Boolean(cli.values.global), Boolean(cli.values.force), Boolean(cli.values.yes));
+                    }
+                    catch (error) {
+                        exitWithError(error);
+                    }
+                    break;
+                }
+                case "help":
+                case undefined: {
+                    console.log("Usage: qmd skill <show|install> [options]");
+                    console.log("");
+                    console.log("Commands:");
+                    console.log("  show                 Print the QMD skill");
+                    console.log("  install              Install QMD skill into ./.agents/skills/qmd");
+                    console.log("");
+                    console.log("Options:");
+                    console.log("  --global             Install into ~/.agents/skills/qmd");
+                    console.log("  --yes                Also create the .claude/skills/qmd symlink");
+                    console.log("  -f, --force          Replace existing install or symlink");
+                    process.exit(0);
+                }
+                default:
+                    console.error(`Unknown subcommand: ${subcommand}`);
+                    console.error("Run 'qmd skill help' for usage");
+                    printDoctorHint();
+                    process.exit(1);
+            }
+            break;
+        }
+        case "cleanup": {
+            const db = getDb();
+            // 1. Clear llm_cache
+            const cacheCount = deleteLLMCache(db);
+            console.log(`${c.green}✓${c.reset} Cleared ${cacheCount} cached API responses`);
+            // 2. Remove orphaned vectors
+            const orphanedVecs = cleanupOrphanedVectors(db);
+            if (orphanedVecs > 0) {
+                console.log(`${c.green}✓${c.reset} Removed ${orphanedVecs} orphaned embedding chunks`);
+            }
+            else {
+                console.log(`${c.dim}No orphaned embeddings to remove${c.reset}`);
+            }
+            // 3. Remove inactive documents
+            const inactiveDocs = deleteInactiveDocuments(db);
+            if (inactiveDocs > 0) {
+                console.log(`${c.green}✓${c.reset} Removed ${inactiveDocs} inactive document records`);
+            }
+            // 4. Vacuum to reclaim space
+            vacuumDatabase(db);
+            console.log(`${c.green}✓${c.reset} Database vacuumed`);
+            closeDb();
+            break;
+        }
+        default:
+            console.error(`Unknown command: ${cli.command}`);
+            console.error("Run 'qmd --help' for usage.");
+            printDoctorHint();
+            process.exit(1);
+    }
+    if (cli.command !== "mcp") {
+        await finishSuccessfulCliCommand({
+            command: cli.command,
+            format: cli.opts.format,
+        });
+    }
+} // end if (main module)