@tobilu/qmd 2.0.1 → 2.5.1

package/dist/cli/qmd.js

@@ -1,32 +1,41 @@
 #!/usr/bin/env node
-import { openDatabase } from "../db.js";
+import { isBun, openDatabase } from "../db.js";
 import fastGlob from "fast-glob";
 import { execSync, spawn as nodeSpawn } from "child_process";
 import { fileURLToPath } from "url";
-import { dirname, join as pathJoin, relative as relativePath } from "path";
+import { basename, dirname, join as pathJoin, relative as relativePath, resolve as pathResolve } from "path";
 import { parseArgs } from "util";
-import { readFileSync, realpathSync, statSync, existsSync, unlinkSync, writeFileSync, openSync, closeSync, mkdirSync, lstatSync, rmSync, symlinkSync, readlinkSync } from "fs";
+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, getHashesForEmbedding, clearAllEmbeddings, insertEmbedding, getStatus, hashContent, extractTitle, formatDocForEmbedding, chunkDocumentByTokens, clearCache, getCacheKey, getCachedResult, setCachedResult, getIndexHealth, parseVirtualPath, buildVirtualPath, isVirtualPath, resolveVirtualPath, toVirtualPath, insertContent, insertDocument, findActiveDocument, updateDocumentTitle, updateDocument, deactivateDocument, getActiveDocumentPaths, cleanupOrphanedContent, deleteLLMCache, deleteInactiveDocuments, cleanupOrphanedVectors, vacuumDatabase, getCollectionsWithoutContext, getTopLevelPathsWithoutContext, handelize, hybridQuery, vectorSearchQuery, structuredSearch, addLineNumbers, DEFAULT_EMBED_MODEL, DEFAULT_RERANK_MODEL, DEFAULT_GLOB, DEFAULT_MULTI_GET_MAX_BYTES, createStore, getDefaultDbPath, reindexCollection, generateEmbeddings, syncConfigToDb, } from "../store.js";
-import { disposeDefaultLlamaCpp, getDefaultLlamaCpp, withLLMSession, pullModels, DEFAULT_EMBED_MODEL_URI, DEFAULT_GENERATE_MODEL_URI, DEFAULT_RERANK_MODEL_URI, DEFAULT_MODEL_CACHE_DIR } from "../llm.js";
+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, generateEmbeddings, maybeAdoptLegacyEmbeddingFingerprint, syncConfigToDb, } from "../store.js";
+import { disposeDefaultLlamaCpp, getDefaultLlamaCpp, setDefaultLlamaCpp, LlamaCpp, withLLMSession, pullModels, DEFAULT_MODEL_CACHE_DIR, resolveEmbedModel, resolveGenerateModel, resolveRerankModel, resolveModels, inspectGgufFile } 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, } from "../collections.js";
-import { getEmbeddedQmdSkillContent, getEmbeddedQmdSkillFiles } from "../embedded-skills.js";
-// Enable production mode - allows using default database path
-// Tests must set INDEX_PATH or use createStore() with explicit path
-enableProductionMode();
+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
@@ -59,16 +68,18 @@ function closeDb() {
 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 { resolve } = require('path');
-        const { cwd } = require('process');
-        const absolutePath = resolve(cwd(), name);
+        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();
@@ -94,6 +105,51 @@ 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());
+    });
+}
+function shouldBypassNativeCleanup(options) {
+    return ((options.platform ?? process.platform) === "darwin" &&
+        options.command === "query" &&
+        options.format === "json" &&
+        process.env.QMD_DISABLE_DARWIN_QUERY_JSON_SAFE_EXIT !== "1");
+}
+function immediateProcessExit(code) {
+    const processWithReallyExit = process;
+    if (typeof processWithReallyExit.reallyExit === "function") {
+        processWithReallyExit.reallyExit(code);
+        return;
+    }
+    process.exit(code);
+}
+/**
+ * Finish a successful CLI command after output has been flushed. On macOS JSON
+ * query runs, skip normal native teardown and use Node/Bun's immediate exit path:
+ * ggml Metal can abort from C++ finalizers after valid JSON has already been
+ * produced (#368). This wrapper is only reached after the command completed, so
+ * real query failures still exit through the normal error path before this runs.
+ */
+export async function finishSuccessfulCliCommand(options) {
+    const stderr = options.stderr ?? process.stderr;
+    const exit = options.exit ?? ((code) => process.exit(code));
+    const immediateExit = options.immediateExit ?? immediateProcessExit;
+    await flushWritable(options.stdout ?? process.stdout);
+    if (shouldBypassNativeCleanup(options)) {
+        await flushWritable(stderr);
+        immediateExit(0);
+        return;
+    }
+    try {
+        await (options.cleanup ?? disposeDefaultLlamaCpp)();
+    }
+    catch (error) {
+        stderr.write(`QMD Warning: cleanup after successful output failed (${error instanceof Error ? error.message : String(error)}); exiting 0 because command output completed.\n`);
+    }
+    await flushWritable(stderr);
+    exit(0);
+}
 // Ensure cursor is restored on exit
 process.on('SIGINT', () => { cursor.show(); process.exit(130); });
 process.on('SIGTERM', () => { cursor.show(); process.exit(143); });
@@ -126,8 +182,8 @@ function formatETA(seconds) {
     return `${Math.floor(seconds / 3600)}h ${Math.floor((seconds % 3600) / 60)}m`;
 }
 // Check index health and print warnings/tips
-function checkIndexHealth(db) {
-    const { needsEmbedding, totalDocs, daysStale } = getIndexHealth(db);
+function checkIndexHealth(db, model = resolveEmbedModelForCli()) {
+    const { needsEmbedding, totalDocs, daysStale } = getIndexHealth(db, model);
     // Warn if many docs need embedding
     if (needsEmbedding > 0) {
         const pct = Math.round((needsEmbedding / totalDocs) * 100);
@@ -198,6 +254,71 @@ function formatBytes(bytes) {
         return `${(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}× ${name}` : name)
+        .join(", ");
+}
+function sanitizeDiagnosticMessage(message) {
+    const home = homedir();
+    return message
+        .replaceAll(home, "~")
+        .replaceAll(process.cwd(), ".")
+        .split("\n")
+        .map(line => line.trim())
+        .filter(Boolean)
+        .slice(0, 3)
+        .join("; ");
+}
 async function showStatus() {
     const dbPath = getDbPath();
     const db = getDb();
@@ -215,7 +336,8 @@ async function showStatus() {
     // Overall stats
     const totalDocs = db.prepare(`SELECT COUNT(*) as count FROM documents WHERE active = 1`).get();
     const vectorCount = db.prepare(`SELECT COUNT(*) as count FROM content_vectors`).get();
-    const needsEmbedding = getHashesNeedingEmbedding(db);
+    const statusEmbedModel = resolveEmbedModelForCli();
+    const needsEmbedding = getHashesNeedingEmbedding(db, undefined, statusEmbedModel);
     // Most recent update across all collections
     const mostRecent = db.prepare(`SELECT MAX(modified_at) as latest FROM documents WHERE active = 1`).get();
     console.log(`${c.bold}QMD Status${c.reset}\n`);
@@ -261,6 +383,34 @@ async function showStatus() {
             context: ctx.context
         });
     }
+    // AST chunking status
+    try {
+        const { getASTStatus } = await import("../ast.js");
+        const ast = await getASTStatus();
+        console.log(`\n${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) {
@@ -306,41 +456,11 @@ async function showStatus() {
             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(DEFAULT_EMBED_MODEL_URI)}`);
-        console.log(`  Reranking:   ${hfLink(DEFAULT_RERANK_MODEL_URI)}`);
-        console.log(`  Generation:  ${hfLink(DEFAULT_GENERATE_MODEL_URI)}`);
-    }
-    // Device / GPU info
-    try {
-        const llm = getDefaultLlamaCpp();
-        const device = await llm.getDeviceInfo();
-        console.log(`\n${c.bold}Device${c.reset}`);
-        if (device.gpu) {
-            console.log(`  GPU:      ${c.green}${device.gpu}${c.reset} (offloading: ${device.gpuOffloading ? 'yes' : 'no'})`);
-            if (device.gpuDevices.length > 0) {
-                // Deduplicate and count GPUs
-                const counts = new Map();
-                for (const name of device.gpuDevices) {
-                    counts.set(name, (counts.get(name) || 0) + 1);
-                }
-                const deviceStr = Array.from(counts.entries())
-                    .map(([name, count]) => count > 1 ? `${count}× ${name}` : name)
-                    .join(', ');
-                console.log(`  Devices:  ${deviceStr}`);
-            }
-            if (device.vram) {
-                console.log(`  VRAM:     ${formatBytes(device.vram.free)} free / ${formatBytes(device.vram.total)} total`);
-            }
-        }
-        else {
-            console.log(`  GPU:      ${c.yellow}none${c.reset} (running on CPU — models will be slow)`);
-            console.log(`  ${c.dim}Tip: Install CUDA, Vulkan, or Metal support for GPU acceleration.${c.reset}`);
-        }
-        console.log(`  CPU:      ${device.cpuCores} math cores`);
-    }
-    catch {
-        // Don't fail status if LLM init fails
+        console.log(`  Embedding:   ${hfLink(activeModels.embed)}`);
+        console.log(`  Reranking:   ${hfLink(activeModels.rerank)}`);
+        console.log(`  Generation:  ${hfLink(activeModels.generate)}`);
     }
     // Tips section
     const tips = [];
@@ -624,7 +744,6 @@ function contextRemove(pathArg) {
     console.log(`${c.green}✓${c.reset} Removed context for: qmd://${detected.collectionName}/${detected.relativePath}`);
 }
 function getDocument(filename, fromLine, maxLines, lineNumbers) {
-    const db = getDb();
     // Parse :linenum suffix from filename (e.g., "file.md:100")
     let inputPath = filename;
     const colonMatch = inputPath.match(/:(\d+)$/);
@@ -635,6 +754,14 @@ function getDocument(filename, fromLine, maxLines, lineNumbers) {
             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);
@@ -787,7 +914,7 @@ function getDocument(filename, fromLine, maxLines, lineNumbers) {
 function multiGet(pattern, maxLines, maxBytes = DEFAULT_MULTI_GET_MAX_BYTES, format = "cli") {
     const db = getDb();
     // Check if it's a comma-separated list or a glob pattern
-    const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?');
+    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)
@@ -1044,8 +1171,35 @@ function listFiles(pathArg) {
     // Parse the path argument
     let collectionName;
     let pathPrefix = null;
-    if (pathArg.startsWith('qmd://')) {
-        // Virtual path format: qmd://collection/path
+    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: ${pathArg}`);
@@ -1055,8 +1209,24 @@ function listFiles(pathArg) {
         collectionName = parsed.collectionName;
         pathPrefix = parsed.path;
     }
+    else if (pathArg.startsWith('/')) {
+        // Raw absolute filesystem path — longest-prefix match against collection names
+        const normalized = pathArg.replace(/\/$/, '');
+        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 {
-        // Just collection name or collection/path
+        // Short collection name or name/path
         const parts = pathArg.split('/');
         collectionName = parts[0] || '';
         if (parts.length > 1) {
@@ -1288,7 +1458,7 @@ async function indexFiles(pwd, globPattern = DEFAULT_GLOB, collectionName, suppr
         try {
             content = readFileSync(filepath, "utf-8");
         }
-        catch (err) {
+        catch {
             // Skip files that can't be read (e.g. iCloud evicted files returning EAGAIN)
             processed++;
             progress.set((processed / total) * 100);
@@ -1301,8 +1471,8 @@ async function indexFiles(pwd, globPattern = DEFAULT_GLOB, collectionName, suppr
         }
         const hash = await hashContent(content);
         const title = extractTitle(content, relativeFile);
-        // Check if document exists in this collection with this path
-        const existing = findActiveDocument(db, collectionName, path);
+        // 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
@@ -1367,42 +1537,109 @@ function renderProgressBar(percent, width = 30) {
     const bar = "█".repeat(filled) + "░".repeat(empty);
     return bar;
 }
-async function vectorIndex(model = DEFAULT_EMBED_MODEL, force = false) {
+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 = getHashesForEmbedding(db);
-    if (hashesToEmbed.length === 0 && !force) {
+    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: ${model}${c.reset}\n`);
+    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;
-            const percent = (info.bytesProcessed / info.totalBytes) * 100;
+            // 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 = info.bytesProcessed / elapsed;
-            const remainingBytes = info.totalBytes - info.bytesProcessed;
-            const etaSec = remainingBytes / bytesPerSec;
+            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 = `${formatBytes(bytesPerSec)}/s`;
-            const eta = elapsed > 2 ? formatETA(etaSec) : "...";
-            const errStr = info.errors > 0 ? ` ${c.yellow}${info.errors} err${c.reset}` : "";
+            const throughput = bytesPerSec > 0 ? `${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}%${c.reset} ${c.dim}${info.chunksEmbedded}/${info.totalChunks}${c.reset}${errStr} ${c.dim}${throughput} ETA ${eta}${c.reset}   `);
+                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();
@@ -1415,7 +1652,13 @@ async function vectorIndex(model = DEFAULT_EMBED_MODEL, force = false) {
         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}⚠ ${result.errors} chunks failed${c.reset}`);
+            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();
@@ -1513,6 +1756,45 @@ function printEmptySearchResults(format, reason = "no_results") {
     }
     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) {
@@ -1520,13 +1802,21 @@ function outputResults(results, query, opts) {
         return;
     }
     // Helper to create qmd:// URI from displayPath
-    const toQmdPath = (displayPath) => `qmd://${displayPath}`;
+    const toQmdPath = (displayPath) => {
+        const [collectionName, ...segments] = displayPath.split("/");
+        if (!collectionName || segments.length === 0) {
+            return `qmd://${displayPath}`;
+        }
+        const indexName = getActiveIndexName();
+        return buildVirtualPath(collectionName, segments.join("/"), indexName === "index" ? undefined : indexName);
+    };
     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 ? extractSnippet(row.body, query, 300, row.chunkPos, undefined, opts.intent).snippet : undefined;
+            let snippet = !opts.full ? snippetInfo.snippet : undefined;
             if (opts.lineNumbers) {
                 if (body)
                     body = addLineNumbers(body);
@@ -1537,6 +1827,7 @@ function outputResults(results, query, opts) {
                 ...(docid && { docid: `#${docid}` }),
                 score: Math.round(row.score * 100) / 100,
                 file: toQmdPath(row.displayPath),
+                line: snippetInfo.line,
                 title: row.title,
                 ...(row.context && { context: row.context }),
                 ...(body && { body }),
@@ -1555,20 +1846,34 @@ function outputResults(results, query, opts) {
         }
     }
     else if (opts.format === "cli") {
+        const editorUriTemplate = getEditorUriTemplate();
+        const linkDb = getDb();
         for (let i = 0; i < filtered.length; i++) {
             const row = filtered[i];
             if (!row)
                 continue;
-            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, undefined, opts.intent);
+            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent);
             const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);
             // Line 1: filepath with docid
-            const path = toQmdPath(row.displayPath);
+            const virtualPath = row.file.startsWith("qmd://") ? row.file : toQmdPath(row.displayPath);
+            const parsed = parseVirtualPath(virtualPath);
+            const absolutePath = resolveVirtualPath(linkDb, virtualPath);
+            const legacyPath = toQmdPath(row.displayPath);
+            const displayPath = parsed?.path || row.displayPath;
             // Only show :line if we actually found a term match in the snippet body (exclude header line).
             const snippetBody = snippet.split("\n").slice(1).join("\n").toLowerCase();
             const hasMatch = query.toLowerCase().split(/\s+/).some(t => t.length > 0 && snippetBody.includes(t));
             const lineInfo = hasMatch ? `:${line}` : "";
             const docidStr = docid ? ` ${c.dim}#${docid}${c.reset}` : "";
-            console.log(`${c.cyan}${path}${c.dim}${lineInfo}${c.reset}${docidStr}`);
+            if (process.stdout.isTTY && absolutePath && parsed?.path) {
+                const linkLine = hasMatch ? line : 1;
+                const linkTarget = buildEditorUri(editorUriTemplate, absolutePath, linkLine, 1);
+                const clickable = termLink(`${displayPath}${lineInfo}`, linkTarget);
+                console.log(`${c.cyan}${clickable}${c.reset}${docidStr}`);
+            }
+            else {
+                console.log(`${c.cyan}${legacyPath}${c.dim}${lineInfo}${c.reset}${docidStr}`);
+            }
             // Line 2: Title (if available)
             if (row.title) {
                 console.log(`${c.bold}Title: ${row.title}${c.reset}`);
@@ -1603,8 +1908,9 @@ function outputResults(results, query, opts) {
             }
             console.log();
             // Snippet with highlighting (diff-style header included)
-            let displaySnippet = opts.lineNumbers ? addLineNumbers(snippet, line) : snippet;
-            const highlighted = highlightTerms(displaySnippet, query);
+            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)
@@ -1618,7 +1924,7 @@ function outputResults(results, query, opts) {
                 continue;
             const heading = row.title || row.displayPath;
             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, undefined, opts.intent).snippet;
+            let content = opts.full ? row.body : extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent).snippet;
             if (opts.lineNumbers) {
                 content = addLineNumbers(content);
             }
@@ -1632,7 +1938,7 @@ function outputResults(results, query, opts) {
             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, undefined, opts.intent).snippet;
+            let content = opts.full ? row.body : extractSnippet(row.body, query, 500, row.chunkPos, row.chunkLen, opts.intent).snippet;
             if (opts.lineNumbers) {
                 content = addLineNumbers(content);
             }
@@ -1643,10 +1949,10 @@ function outputResults(results, query, opts) {
         // CSV format
         console.log("docid,score,file,title,context,line,snippet");
         for (const row of filtered) {
-            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, undefined, opts.intent);
+            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, line);
+                content = addLineNumbers(content, opts.full ? 1 : line);
             }
             const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
             const snippetText = content || "";
@@ -1867,8 +2173,10 @@ async function querySearch(query, opts, _embedModel = DEFAULT_EMBED_MODEL, _rera
                 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}`);
@@ -1894,8 +2202,10 @@ async function querySearch(query, opts, _embedModel = DEFAULT_EMBED_MODEL, _rera
                 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`);
@@ -1942,13 +2252,13 @@ async function querySearch(query, opts, _embedModel = DEFAULT_EMBED_MODEL, _rera
         const displayQuery = structuredQueries
             ? (structuredQueries.find(s => s.type === 'lex')?.query || structuredQueries.find(s => s.type === 'vec')?.query || query)
             : query;
-        // Map to CLI output format — use bestChunk for snippet display
         outputResults(results.map(r => ({
             file: r.file,
             displayPath: r.displayPath,
             title: r.title,
-            body: r.bestChunk,
+            body: r.body,
             chunkPos: r.bestChunkPos,
+            chunkLen: r.bestChunk.length,
             score: r.score,
             context: r.context,
             docid: r.docid,
@@ -1990,6 +2300,8 @@ function parseCLI() {
             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" },
@@ -2000,7 +2312,11 @@ function parseCLI() {
             "line-numbers": { type: "boolean" }, // add line numbers to output
             // 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" },
@@ -2009,11 +2325,27 @@ function parseCLI() {
         allowPositionals: true,
         strict: false, // Allow unknown options to pass through
     });
-    // Select index name (default: "index")
+    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
     let format = "cli";
@@ -2040,8 +2372,10 @@ function parseCLI() {
         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"]),
     };
     return {
         command: positionals[0] || "",
@@ -2079,26 +2413,293 @@ function removePath(path) {
         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() {
-    console.log("QMD Skill (embedded)");
+    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 = getEmbeddedQmdSkillContent();
+    const content = readSkillContent(skill);
     process.stdout.write(content.endsWith("\n") ? content : content + "\n");
 }
-function writeEmbeddedSkill(targetDir, force) {
+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);
     }
-    mkdirSync(targetDir, { recursive: true });
-    for (const file of getEmbeddedQmdSkillFiles()) {
-        const destination = resolve(targetDir, file.relativePath);
-        mkdirSync(dirname(destination), { recursive: true });
-        writeFileSync(destination, file.content, "utf-8");
+    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)) {
@@ -2148,7 +2749,7 @@ async function shouldCreateClaudeSymlink(linkPath, autoYes) {
 }
 async function installSkill(globalInstall, force, autoYes) {
     const installDir = getSkillInstallDir(globalInstall);
-    writeEmbeddedSkill(installDir, force);
+    writeSkillInstall(installDir, force);
     console.log(`✓ Installed QMD skill to ${installDir}`);
     const claudeLinkPath = getClaudeSkillLinkPath(globalInstall);
     if (!(await shouldCreateClaudeSymlink(claudeLinkPath, autoYes))) {
@@ -2175,8 +2776,10 @@ function showHelp() {
     console.log("  qmd vsearch <query>           - Vector similarity only");
     console.log("  qmd get <file>[:line] [-l N]  - Show a single document, optional line slice");
     console.log("  qmd multi-get <pattern>       - Batch fetch via glob or comma-separated list");
-    console.log("  qmd skill show/install        - Show or install the packaged QMD skill");
+    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");
@@ -2184,9 +2787,12 @@ function showHelp() {
     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]                - Generate/refresh vector embeddings");
+    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):");
@@ -2225,6 +2831,7 @@ function showHelp() {
     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`.");
@@ -2232,6 +2839,7 @@ function showHelp() {
     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 --files/--json)");
@@ -2239,11 +2847,16 @@ function showHelp() {
     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 in output");
     console.log("  --explain                  - Include retrieval score traces (query --json/CLI)");
     console.log("  --files | --json | --csv | --md | --xml  - Output format");
     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)");
@@ -2251,10 +2864,531 @@ function showHelp() {
     console.log("");
     console.log(`Index: ${getDbPath()}`);
 }
-async function showVersion() {
+function doctorCheck(label, ok, details) {
+    const mark = ok ? `${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_DISABLE_DARWIN_QUERY_JSON_SAFE_EXIT", "disables macOS JSON-query safe exit workaround; may re-expose Metal finalizer crashes");
+    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`.");
+            }
+        }
+        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));
+    }
+    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");
-    const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
+    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();
@@ -2273,6 +3407,10 @@ const isMain = argv1 === __filename
     || 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();
@@ -2286,8 +3424,8 @@ if (isMain) {
         console.log("Usage: qmd skill <show|install> [options]");
         console.log("");
         console.log("Commands:");
-        console.log("  show                 Print the packaged QMD skill");
-        console.log("  install              Install into ./.agents/skills/qmd");
+        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");
@@ -2522,25 +3660,57 @@ if (isMain) {
                 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":
-            await vectorIndex(DEFAULT_EMBED_MODEL, !!cli.values.force);
+            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 = [
-                DEFAULT_EMBED_MODEL_URI,
-                DEFAULT_GENERATE_MODEL_URI,
-                DEFAULT_RERANK_MODEL_URI,
+                activeModels.embed,
+                activeModels.generate,
+                activeModels.rerank,
             ];
             console.log(`${c.bold}Pulling models${c.reset}`);
             const results = await pullModels(models, {
@@ -2581,6 +3751,25 @@ if (isMain) {
             }
             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
@@ -2626,9 +3815,10 @@ if (isMain) {
                     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, "mcp", "--http", "--port", String(port)]
-                        : [selfPath, "mcp", "--http", "--port", String(port)];
+                        ? ["--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,
@@ -2646,10 +3836,10 @@ if (isMain) {
                 process.removeAllListeners("SIGINT");
                 const { startMcpHttpServer } = await import("../mcp/server.js");
                 try {
-                    await startMcpHttpServer(port);
+                    await startMcpHttpServer(port, { dbPath: getDbPath() });
                 }
                 catch (e) {
-                    if (e?.code === "EADDRINUSE") {
+                    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);
                     }
@@ -2659,7 +3849,27 @@ if (isMain) {
             else {
                 // Default: stdio transport
                 const { startMcpServer } = await import("../mcp/server.js");
-                await startMcpServer();
+                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;
         }
@@ -2675,8 +3885,7 @@ if (isMain) {
                         await installSkill(Boolean(cli.values.global), Boolean(cli.values.force), Boolean(cli.values.yes));
                     }
                     catch (error) {
-                        console.error(error instanceof Error ? error.message : String(error));
-                        process.exit(1);
+                        exitWithError(error);
                     }
                     break;
                 }
@@ -2685,8 +3894,8 @@ if (isMain) {
                     console.log("Usage: qmd skill <show|install> [options]");
                     console.log("");
                     console.log("Commands:");
-                    console.log("  show                 Print the packaged QMD skill");
-                    console.log("  install              Install into ./.agents/skills/qmd");
+                    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");
@@ -2697,6 +3906,7 @@ if (isMain) {
                 default:
                     console.error(`Unknown subcommand: ${subcommand}`);
                     console.error("Run 'qmd skill help' for usage");
+                    printDoctorHint();
                     process.exit(1);
             }
             break;
@@ -2728,10 +3938,13 @@ if (isMain) {
         default:
             console.error(`Unknown command: ${cli.command}`);
             console.error("Run 'qmd --help' for usage.");
+            printDoctorHint();
             process.exit(1);
     }
     if (cli.command !== "mcp") {
-        await disposeDefaultLlamaCpp();
-        process.exit(0);
+        await finishSuccessfulCliCommand({
+            command: cli.command,
+            format: cli.opts.format,
+        });
     }
 } // end if (main module)