#!/usr/bin/env node
import { 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 { parseArgs } from "util";
import { readFileSync, realpathSync, statSync, existsSync, unlinkSync, writeFileSync, openSync, closeSync, mkdirSync, lstatSync, rmSync, symlinkSync, readlinkSync } from "fs";
import { createInterface } from "readline/promises";
import { getPwd, getRealPath, homedir, resolve, enableProductionMode, searchFTS, extractSnippet, getContextForFile, getContextForPath, listCollections, removeCollection, renameCollection, findSimilarFiles, findDocumentByDocid, isDocid, matchFilesByGlob, getHashesNeedingEmbedding, clearAllEmbeddings, insertEmbedding, getStatus, hashContent, extractTitle, formatDocForEmbedding, 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_EMBED_MAX_BATCH_BYTES, DEFAULT_EMBED_MAX_DOCS_PER_BATCH, DEFAULT_RERANK_MODEL, DEFAULT_GLOB, DEFAULT_MULTI_GET_MAX_BYTES, createStore, getDefaultDbPath, reindexCollection, generateEmbeddings, syncConfigToDb, } from "../store.js";
import { disposeDefaultLlamaCpp, getDefaultLlamaCpp, setDefaultLlamaCpp, LlamaCpp, withLLMSession, pullModels, DEFAULT_EMBED_MODEL_URI, DEFAULT_GENERATE_MODEL_URI, DEFAULT_RERANK_MODEL_URI, DEFAULT_MODEL_CACHE_DIR } 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";
import { createEmbeddingProvider, resolveProviderKind, ModelMismatchError, } from "../embedding/index.js";
// Enable production mode - allows using default database path
// Tests must set INDEX_PATH or use createStore() with explicit path
enableProductionMode();
// =============================================================================
// Store/DB lifecycle (no legacy singletons in store.ts)
// =============================================================================
let store = null;
let storeDbPathOverride;
function getStore() {
    if (!store) {
        store = createStore(storeDbPathOverride);
        // Sync YAML config into SQLite store_collections so store.ts reads from DB
        try {
            const config = loadConfig();
            syncConfigToDb(store.db, config);
            if (config.models) {
                setDefaultLlamaCpp(new LlamaCpp({
                    embedModel: config.models.embed,
                    generateModel: config.models.generate,
                    rerankModel: config.models.rerank,
                }));
            }
        }
        catch {
            // Config may not exist yet — that's fine, DB works without it
        }
    }
    return store;
}
function getDb() {
    return getStore().db;
}
/** Re-sync YAML config into SQLite after CLI mutations (add/remove/rename collection, context changes) */
function resyncConfig() {
    const s = getStore();
    try {
        const config = loadConfig();
        // Clear config hash to force re-sync
        s.db.prepare(`DELETE FROM store_config WHERE key = 'config_hash'`).run();
        syncConfigToDb(s.db, config);
    }
    catch {
        // Config may not exist — that's fine
    }
}
function closeDb() {
    if (store) {
        store.close();
        store = null;
    }
}
function getDbPath() {
    return store?.dbPath ?? storeDbPathOverride ?? getDefaultDbPath();
}
function 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);
        // Replace path separators with underscores to create a valid filename
        normalizedName = absolutePath.replace(/\//g, '_').replace(/^_/, '');
    }
    storeDbPathOverride = normalizedName ? getDefaultDbPath(normalizedName) : undefined;
    // Reset open handle so next use opens the new index
    closeDb();
}
function ensureVecTable(_db, dimensions) {
    // Store owns the DB; ignore `_db` and ensure vec table on the active store
    getStore().ensureVecTable(dimensions);
}
// Terminal colors (respects NO_COLOR env)
const useColor = !process.env.NO_COLOR && process.stdout.isTTY;
const c = {
    reset: useColor ? "\x1b[0m" : "",
    dim: useColor ? "\x1b[2m" : "",
    bold: useColor ? "\x1b[1m" : "",
    cyan: useColor ? "\x1b[36m" : "",
    yellow: useColor ? "\x1b[33m" : "",
    green: useColor ? "\x1b[32m" : "",
    magenta: useColor ? "\x1b[35m" : "",
    blue: useColor ? "\x1b[34m" : "",
    red: useColor ? "\x1b[31m" : "",
};
// Terminal cursor control
const cursor = {
    hide() { process.stderr.write('\x1b[?25l'); },
    show() { process.stderr.write('\x1b[?25h'); },
};
// Ensure cursor is restored on exit
process.on('SIGINT', () => { cursor.show(); process.exit(130); });
process.on('SIGTERM', () => { cursor.show(); process.exit(143); });
// Terminal progress bar using OSC 9;4 escape sequence (TTY only)
const isTTY = process.stderr.isTTY;
const progress = {
    set(percent) {
        if (isTTY)
            process.stderr.write(`\x1b]9;4;1;${Math.round(percent)}\x07`);
    },
    clear() {
        if (isTTY)
            process.stderr.write(`\x1b]9;4;0\x07`);
    },
    indeterminate() {
        if (isTTY)
            process.stderr.write(`\x1b]9;4;3\x07`);
    },
    error() {
        if (isTTY)
            process.stderr.write(`\x1b]9;4;2\x07`);
    },
};
// Format seconds into human-readable ETA
function formatETA(seconds) {
    if (seconds < 60)
        return `${Math.round(seconds)}s`;
    if (seconds < 3600)
        return `${Math.floor(seconds / 60)}m ${Math.round(seconds % 60)}s`;
    return `${Math.floor(seconds / 3600)}h ${Math.floor((seconds % 3600) / 60)}m`;
}
// Check index health and print warnings/tips
function checkIndexHealth(db) {
    const { needsEmbedding, totalDocs, daysStale } = getIndexHealth(db);
    // Warn if many docs need embedding
    if (needsEmbedding > 0) {
        const pct = Math.round((needsEmbedding / totalDocs) * 100);
        if (pct >= 10) {
            process.stderr.write(`${c.yellow}Warning: ${needsEmbedding} documents (${pct}%) need embeddings. Run 'qmd embed' for better results.${c.reset}\n`);
        }
        else {
            process.stderr.write(`${c.dim}Tip: ${needsEmbedding} documents need embeddings. Run 'qmd embed' to index them.${c.reset}\n`);
        }
    }
    // Check if most recent document update is older than 2 weeks
    if (daysStale !== null && daysStale >= 14) {
        process.stderr.write(`${c.dim}Tip: Index last updated ${daysStale} days ago. Run 'qmd update' to refresh.${c.reset}\n`);
    }
}
// Compute unique display path for a document
// Always include at least parent folder + filename, add more parent dirs until unique
function computeDisplayPath(filepath, collectionPath, existingPaths) {
    // Get path relative to collection (include collection dir name)
    const collectionDir = collectionPath.replace(/\/$/, '');
    const collectionName = collectionDir.split('/').pop() || '';
    let relativePath;
    if (filepath.startsWith(collectionDir + '/')) {
        // filepath is under collection: use collection name + relative path
        relativePath = collectionName + filepath.slice(collectionDir.length);
    }
    else {
        // Fallback: just use the filepath
        relativePath = filepath;
    }
    const parts = relativePath.split('/').filter(p => p.length > 0);
    // Always include at least parent folder + filename (minimum 2 parts if available)
    // Then add more parent dirs until unique
    const minParts = Math.min(2, parts.length);
    for (let i = parts.length - minParts; i >= 0; i--) {
        const candidate = parts.slice(i).join('/');
        if (!existingPaths.has(candidate)) {
            return candidate;
        }
    }
    // Absolute fallback: use full path (should be unique)
    return filepath;
}
function formatTimeAgo(date) {
    const seconds = Math.floor((Date.now() - date.getTime()) / 1000);
    if (seconds < 60)
        return `${seconds}s ago`;
    const minutes = Math.floor(seconds / 60);
    if (minutes < 60)
        return `${minutes}m ago`;
    const hours = Math.floor(minutes / 60);
    if (hours < 24)
        return `${hours}h ago`;
    const days = Math.floor(hours / 24);
    return `${days}d ago`;
}
function formatMs(ms) {
    if (ms < 1000)
        return `${ms}ms`;
    return `${(ms / 1000).toFixed(1)}s`;
}
function formatBytes(bytes) {
    if (bytes < 1024)
        return `${bytes} B`;
    if (bytes < 1024 * 1024)
        return `${(bytes / 1024).toFixed(1)} KB`;
    if (bytes < 1024 * 1024 * 1024)
        return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
    return `${(bytes / (1024 * 1024 * 1024)).toFixed(1)} GB`;
}
async function showStatus() {
    const dbPath = getDbPath();
    const db = getDb();
    // Collections are defined in YAML; no duplicate cleanup needed.
    // Collections are defined in YAML; no duplicate cleanup needed.
    // Index size
    let indexSize = 0;
    try {
        const stat = statSync(dbPath).size;
        indexSize = stat;
    }
    catch { }
    // Collections info (from YAML + database stats)
    const collections = listCollections(db);
    // Overall stats
    const totalDocs = db.prepare(`SELECT COUNT(*) as count FROM documents WHERE active = 1`).get();
    const vectorCount = db.prepare(`SELECT COUNT(*) as count FROM content_vectors`).get();
    const needsEmbedding = getHashesNeedingEmbedding(db);
    // Most recent update across all collections
    const mostRecent = db.prepare(`SELECT MAX(modified_at) as latest FROM documents WHERE active = 1`).get();
    console.log(`${c.bold}QMD Status${c.reset}\n`);
    console.log(`Index: ${dbPath}`);
    console.log(`Size:  ${formatBytes(indexSize)}`);
    // MCP daemon status (check PID file liveness)
    const mcpCacheDir = process.env.XDG_CACHE_HOME
        ? resolve(process.env.XDG_CACHE_HOME, "qmd")
        : resolve(homedir(), ".cache", "qmd");
    const mcpPidPath = resolve(mcpCacheDir, "mcp.pid");
    if (existsSync(mcpPidPath)) {
        const mcpPid = parseInt(readFileSync(mcpPidPath, "utf-8").trim());
        try {
            process.kill(mcpPid, 0);
            console.log(`MCP:   ${c.green}running${c.reset} (PID ${mcpPid})`);
        }
        catch {
            unlinkSync(mcpPidPath);
            // Stale PID file cleaned up silently
        }
    }
    console.log("");
    console.log(`${c.bold}Documents${c.reset}`);
    console.log(`  Total:    ${totalDocs.count} files indexed`);
    console.log(`  Vectors:  ${vectorCount.count} embedded`);
    if (needsEmbedding > 0) {
        console.log(`  ${c.yellow}Pending:  ${needsEmbedding} need embedding${c.reset} (run 'qmd embed')`);
    }
    if (mostRecent.latest) {
        const lastUpdate = new Date(mostRecent.latest);
        console.log(`  Updated:  ${formatTimeAgo(lastUpdate)}`);
    }
    // Get all contexts grouped by collection (from YAML)
    const allContexts = listAllContexts();
    const contextsByCollection = new Map();
    for (const ctx of allContexts) {
        // Group contexts by collection name
        if (!contextsByCollection.has(ctx.collection)) {
            contextsByCollection.set(ctx.collection, []);
        }
        contextsByCollection.get(ctx.collection).push({
            path_prefix: ctx.path,
            context: ctx.context
        });
    }
    // AST chunking status
    try {
        const { getASTStatus } = await import("../ast.js");
        const ast = await getASTStatus();
        console.log(`\n${c.bold}AST Chunking${c.reset}`);
        if (ast.available) {
            const ok = ast.languages.filter(l => l.available).map(l => l.language);
            const fail = ast.languages.filter(l => !l.available);
            console.log(`  Status:   ${c.green}active${c.reset}`);
            console.log(`  Languages: ${ok.join(", ")}`);
            if (fail.length > 0) {
                for (const f of fail) {
                    console.log(`  ${c.yellow}Unavailable: ${f.language} (${f.error})${c.reset}`);
                }
            }
        }
        else {
            console.log(`  Status:   ${c.yellow}unavailable${c.reset} (falling back to regex chunking)`);
            for (const l of ast.languages) {
                if (l.error)
                    console.log(`  ${c.dim}${l.language}: ${l.error}${c.reset}`);
            }
        }
    }
    catch {
        console.log(`\n${c.bold}AST Chunking${c.reset}`);
        console.log(`  Status:   ${c.dim}not available${c.reset}`);
    }
    if (collections.length > 0) {
        console.log(`\n${c.bold}Collections${c.reset}`);
        for (const col of collections) {
            const lastMod = col.last_modified ? formatTimeAgo(new Date(col.last_modified)) : "never";
            const contexts = contextsByCollection.get(col.name) || [];
            console.log(`  ${c.cyan}${col.name}${c.reset} ${c.dim}(qmd://${col.name}/)${c.reset}`);
            console.log(`    ${c.dim}Pattern:${c.reset}  ${col.glob_pattern}`);
            console.log(`    ${c.dim}Files:${c.reset}    ${col.active_count} (updated ${lastMod})`);
            if (contexts.length > 0) {
                console.log(`    ${c.dim}Contexts:${c.reset} ${contexts.length}`);
                for (const ctx of contexts) {
                    // Handle both empty string and '/' as root context
                    const pathDisplay = (ctx.path_prefix === '' || ctx.path_prefix === '/') ? '/' : `/${ctx.path_prefix}`;
                    const contextPreview = ctx.context.length > 60
                        ? ctx.context.substring(0, 57) + '...'
                        : ctx.context;
                    console.log(`      ${c.dim}${pathDisplay}:${c.reset} ${contextPreview}`);
                }
            }
        }
        // Show examples of virtual paths
        console.log(`\n${c.bold}Examples${c.reset}`);
        console.log(`  ${c.dim}# List files in a collection${c.reset}`);
        if (collections.length > 0 && collections[0]) {
            console.log(`  qmd ls ${collections[0].name}`);
        }
        console.log(`  ${c.dim}# Get a document${c.reset}`);
        if (collections.length > 0 && collections[0]) {
            console.log(`  qmd get qmd://${collections[0].name}/path/to/file.md`);
        }
        console.log(`  ${c.dim}# Search within a collection${c.reset}`);
        if (collections.length > 0 && collections[0]) {
            console.log(`  qmd search "query" -c ${collections[0].name}`);
        }
    }
    else {
        console.log(`\n${c.dim}No collections. Run 'qmd collection add .' to index markdown files.${c.reset}`);
    }
    // Models
    {
        // hf:org/repo/file.gguf → https://huggingface.co/org/repo
        const hfLink = (uri) => {
            const match = uri.match(/^hf:([^/]+\/[^/]+)\//);
            return match ? `https://huggingface.co/${match[1]}` : uri;
        };
        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:      ${device.cpuCores} math cores`);
    }
    catch {
        // Don't fail status if LLM init fails
    }
    // Tips section
    const tips = [];
    // Check for collections without context
    const collectionsWithoutContext = collections.filter(col => {
        const contexts = contextsByCollection.get(col.name) || [];
        return contexts.length === 0;
    });
    if (collectionsWithoutContext.length > 0) {
        const names = collectionsWithoutContext.map(c => c.name).slice(0, 3).join(', ');
        const more = collectionsWithoutContext.length > 3 ? ` +${collectionsWithoutContext.length - 3} more` : '';
        tips.push(`Add context to collections for better search results: ${names}${more}`);
        tips.push(`  ${c.dim}qmd context add qmd://<name>/ "What this collection contains"${c.reset}`);
        tips.push(`  ${c.dim}qmd context add qmd://<name>/meeting-notes "Weekly team meeting notes"${c.reset}`);
    }
    // Check for collections without update commands
    const collectionsWithoutUpdate = collections.filter(col => {
        const yamlCol = getCollectionFromYaml(col.name);
        return !yamlCol?.update;
    });
    if (collectionsWithoutUpdate.length > 0 && collections.length > 1) {
        const names = collectionsWithoutUpdate.map(c => c.name).slice(0, 3).join(', ');
        const more = collectionsWithoutUpdate.length > 3 ? ` +${collectionsWithoutUpdate.length - 3} more` : '';
        tips.push(`Add update commands to keep collections fresh: ${names}${more}`);
        tips.push(`  ${c.dim}qmd collection update-cmd <name> 'git stash && git pull --rebase --ff-only && git stash pop'${c.reset}`);
    }
    if (tips.length > 0) {
        console.log(`\n${c.bold}Tips${c.reset}`);
        for (const tip of tips) {
            console.log(`  ${tip}`);
        }
    }
    closeDb();
}
async function updateCollections() {
    const db = getDb();
    const storeInstance = getStore();
    // Collections are defined in YAML; no duplicate cleanup needed.
    // Clear Ollama cache on update
    clearCache(db);
    const collections = listCollections(db);
    if (collections.length === 0) {
        console.log(`${c.dim}No collections found. Run 'qmd collection add .' to index markdown files.${c.reset}`);
        closeDb();
        return;
    }
    console.log(`${c.bold}Updating ${collections.length} collection(s)...${c.reset}\n`);
    for (let i = 0; i < collections.length; i++) {
        const col = collections[i];
        if (!col)
            continue;
        console.log(`${c.cyan}[${i + 1}/${collections.length}]${c.reset} ${c.bold}${col.name}${c.reset} ${c.dim}(${col.glob_pattern})${c.reset}`);
        // Execute custom update command if specified in YAML
        const yamlCol = getCollectionFromYaml(col.name);
        if (yamlCol?.update) {
            console.log(`${c.dim}    Running update command: ${yamlCol.update}${c.reset}`);
            try {
                const proc = nodeSpawn("bash", ["-c", yamlCol.update], {
                    cwd: col.pwd,
                    stdio: ["ignore", "pipe", "pipe"],
                });
                const [output, errorOutput, exitCode] = await new Promise((resolve, reject) => {
                    let out = "";
                    let err = "";
                    proc.stdout?.on("data", (d) => { out += d.toString(); });
                    proc.stderr?.on("data", (d) => { err += d.toString(); });
                    proc.on("error", reject);
                    proc.on("close", (code) => resolve([out, err, code ?? 1]));
                });
                if (output.trim()) {
                    console.log(output.trim().split('\n').map(l => `    ${l}`).join('\n'));
                }
                if (errorOutput.trim()) {
                    console.log(errorOutput.trim().split('\n').map(l => `    ${l}`).join('\n'));
                }
                if (exitCode !== 0) {
                    console.log(`${c.yellow}✗ Update command failed with exit code ${exitCode}${c.reset}`);
                    process.exit(exitCode);
                }
            }
            catch (err) {
                console.log(`${c.yellow}✗ Update command failed: ${err}${c.reset}`);
                process.exit(1);
            }
        }
        const startTime = Date.now();
        console.log(`Collection: ${col.pwd} (${col.glob_pattern})`);
        progress.indeterminate();
        const result = await reindexCollection(storeInstance, col.pwd, col.glob_pattern, col.name, {
            ignorePatterns: yamlCol?.ignore,
            onProgress: (info) => {
                progress.set((info.current / info.total) * 100);
                const elapsed = (Date.now() - startTime) / 1000;
                const rate = info.current / elapsed;
                const remaining = (info.total - info.current) / rate;
                const eta = info.current > 2 ? ` ETA: ${formatETA(remaining)}` : "";
                if (isTTY)
                    process.stderr.write(`\rIndexing: ${info.current}/${info.total}${eta}        `);
            },
        });
        progress.clear();
        console.log(`\nIndexed: ${result.indexed} new, ${result.updated} updated, ${result.unchanged} unchanged, ${result.removed} removed`);
        if (result.orphanedCleaned > 0) {
            console.log(`Cleaned up ${result.orphanedCleaned} orphaned content hash(es)`);
        }
        console.log("");
    }
    // Check if any documents need embedding (show once at end)
    const needsEmbedding = getHashesNeedingEmbedding(db);
    closeDb();
    console.log(`${c.green}✓ All collections updated.${c.reset}`);
    if (needsEmbedding > 0) {
        console.log(`\nRun 'qmd embed' to update embeddings (${needsEmbedding} unique hashes need vectors)`);
    }
}
/**
 * Detect which collection (if any) contains the given filesystem path.
 * Returns { collectionId, collectionName, relativePath } or null if not in any collection.
 */
function detectCollectionFromPath(db, fsPath) {
    const realPath = getRealPath(fsPath);
    // Find collections that this path is under from YAML
    const allCollections = yamlListCollections();
    // Find longest matching path
    let bestMatch = null;
    for (const coll of allCollections) {
        if (realPath.startsWith(coll.path + '/') || realPath === coll.path) {
            if (!bestMatch || coll.path.length > bestMatch.path.length) {
                bestMatch = { name: coll.name, path: coll.path };
            }
        }
    }
    if (!bestMatch)
        return null;
    // Calculate relative path
    let relativePath = realPath;
    if (relativePath.startsWith(bestMatch.path + '/')) {
        relativePath = relativePath.slice(bestMatch.path.length + 1);
    }
    else if (relativePath === bestMatch.path) {
        relativePath = '';
    }
    return {
        collectionName: bestMatch.name,
        relativePath
    };
}
async function contextAdd(pathArg, contextText) {
    const db = getDb();
    // Handle "/" as global context (applies to all collections)
    if (pathArg === '/') {
        setGlobalContext(contextText);
        resyncConfig();
        console.log(`${c.green}✓${c.reset} Set global context`);
        console.log(`${c.dim}Context: ${contextText}${c.reset}`);
        closeDb();
        return;
    }
    // Resolve path - defaults to current directory if not provided
    let fsPath = pathArg || '.';
    if (fsPath === '.' || fsPath === './') {
        fsPath = getPwd();
    }
    else if (fsPath.startsWith('~/')) {
        fsPath = homedir() + fsPath.slice(1);
    }
    else if (!fsPath.startsWith('/') && !fsPath.startsWith('qmd://')) {
        fsPath = resolve(getPwd(), fsPath);
    }
    // Handle virtual paths (qmd://collection/path)
    if (isVirtualPath(fsPath)) {
        const parsed = parseVirtualPath(fsPath);
        if (!parsed) {
            console.error(`${c.yellow}Invalid virtual path: ${fsPath}${c.reset}`);
            process.exit(1);
        }
        const coll = getCollectionFromYaml(parsed.collectionName);
        if (!coll) {
            console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
            process.exit(1);
        }
        yamlAddContext(parsed.collectionName, parsed.path, contextText);
        resyncConfig();
        const displayPath = parsed.path
            ? `qmd://${parsed.collectionName}/${parsed.path}`
            : `qmd://${parsed.collectionName}/ (collection root)`;
        console.log(`${c.green}✓${c.reset} Added context for: ${displayPath}`);
        console.log(`${c.dim}Context: ${contextText}${c.reset}`);
        closeDb();
        return;
    }
    // Detect collection from filesystem path
    const detected = detectCollectionFromPath(db, fsPath);
    if (!detected) {
        console.error(`${c.yellow}Path is not in any indexed collection: ${fsPath}${c.reset}`);
        console.error(`${c.dim}Run 'qmd status' to see indexed collections${c.reset}`);
        process.exit(1);
    }
    yamlAddContext(detected.collectionName, detected.relativePath, contextText);
    resyncConfig();
    const displayPath = detected.relativePath ? `qmd://${detected.collectionName}/${detected.relativePath}` : `qmd://${detected.collectionName}/`;
    console.log(`${c.green}✓${c.reset} Added context for: ${displayPath}`);
    console.log(`${c.dim}Context: ${contextText}${c.reset}`);
    closeDb();
}
function contextList() {
    const db = getDb();
    const allContexts = listAllContexts();
    if (allContexts.length === 0) {
        console.log(`${c.dim}No contexts configured. Use 'qmd context add' to add one.${c.reset}`);
        closeDb();
        return;
    }
    console.log(`\n${c.bold}Configured Contexts${c.reset}\n`);
    let lastCollection = '';
    for (const ctx of allContexts) {
        if (ctx.collection !== lastCollection) {
            console.log(`${c.cyan}${ctx.collection}${c.reset}`);
            lastCollection = ctx.collection;
        }
        const displayPath = ctx.path ? `  ${ctx.path}` : '  / (root)';
        console.log(`${displayPath}`);
        console.log(`    ${c.dim}${ctx.context}${c.reset}`);
    }
    closeDb();
}
function contextRemove(pathArg) {
    if (pathArg === '/') {
        // Remove global context
        setGlobalContext(undefined);
        // Resync so SQLite store_config is updated
        const s = getStore();
        resyncConfig();
        closeDb();
        console.log(`${c.green}✓${c.reset} Removed global context`);
        return;
    }
    // Handle virtual paths
    if (isVirtualPath(pathArg)) {
        const parsed = parseVirtualPath(pathArg);
        if (!parsed) {
            console.error(`${c.yellow}Invalid virtual path: ${pathArg}${c.reset}`);
            process.exit(1);
        }
        const coll = getCollectionFromYaml(parsed.collectionName);
        if (!coll) {
            console.error(`${c.yellow}Collection not found: ${parsed.collectionName}${c.reset}`);
            process.exit(1);
        }
        const success = yamlRemoveContext(coll.name, parsed.path);
        if (!success) {
            console.error(`${c.yellow}No context found for: ${pathArg}${c.reset}`);
            process.exit(1);
        }
        console.log(`${c.green}✓${c.reset} Removed context for: ${pathArg}`);
        return;
    }
    // Handle filesystem paths
    let fsPath = pathArg;
    if (fsPath === '.' || fsPath === './') {
        fsPath = getPwd();
    }
    else if (fsPath.startsWith('~/')) {
        fsPath = homedir() + fsPath.slice(1);
    }
    else if (!fsPath.startsWith('/')) {
        fsPath = resolve(getPwd(), fsPath);
    }
    const db = getDb();
    const detected = detectCollectionFromPath(db, fsPath);
    closeDb();
    if (!detected) {
        console.error(`${c.yellow}Path is not in any indexed collection: ${fsPath}${c.reset}`);
        process.exit(1);
    }
    const success = yamlRemoveContext(detected.collectionName, detected.relativePath);
    if (!success) {
        console.error(`${c.yellow}No context found for: qmd://${detected.collectionName}/${detected.relativePath}${c.reset}`);
        process.exit(1);
    }
    console.log(`${c.green}✓${c.reset} Removed context for: qmd://${detected.collectionName}/${detected.relativePath}`);
}
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+)$/);
    if (colonMatch && !fromLine) {
        const matched = colonMatch[1];
        if (matched) {
            fromLine = parseInt(matched, 10);
            inputPath = inputPath.slice(0, -colonMatch[0].length);
        }
    }
    // Handle docid lookup (#abc123, abc123, "#abc123", "abc123", etc.)
    if (isDocid(inputPath)) {
        const docidMatch = findDocumentByDocid(db, inputPath);
        if (docidMatch) {
            inputPath = docidMatch.filepath;
        }
        else {
            console.error(`Document not found: ${filename}`);
            closeDb();
            process.exit(1);
        }
    }
    let doc = null;
    let virtualPath;
    // Handle virtual paths (qmd://collection/path)
    if (isVirtualPath(inputPath)) {
        const parsed = parseVirtualPath(inputPath);
        if (!parsed) {
            console.error(`Invalid virtual path: ${inputPath}`);
            closeDb();
            process.exit(1);
        }
        // Try exact match on collection + path
        doc = db.prepare(`
      SELECT d.collection as collectionName, d.path, content.doc as body
      FROM documents d
      JOIN content ON content.hash = d.hash
      WHERE d.collection = ? AND d.path = ? AND d.active = 1
    `).get(parsed.collectionName, parsed.path);
        if (!doc) {
            // Try fuzzy match by path ending
            doc = db.prepare(`
        SELECT d.collection as collectionName, d.path, content.doc as body
        FROM documents d
        JOIN content ON content.hash = d.hash
        WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
        LIMIT 1
      `).get(parsed.collectionName, `%${parsed.path}`);
        }
        virtualPath = inputPath;
    }
    else {
        // Try to interpret as collection/path format first (before filesystem path)
        // If path is relative (no / or ~ prefix), check if first component is a collection name
        if (!inputPath.startsWith('/') && !inputPath.startsWith('~')) {
            const parts = inputPath.split('/');
            if (parts.length >= 2) {
                const possibleCollection = parts[0];
                const possiblePath = parts.slice(1).join('/');
                // Check if this collection exists
                const collExists = possibleCollection ? db.prepare(`
          SELECT 1 FROM documents WHERE collection = ? AND active = 1 LIMIT 1
        `).get(possibleCollection) : null;
                if (collExists) {
                    // Try exact match on collection + path
                    doc = db.prepare(`
            SELECT d.collection as collectionName, d.path, content.doc as body
            FROM documents d
            JOIN content ON content.hash = d.hash
            WHERE d.collection = ? AND d.path = ? AND d.active = 1
          `).get(possibleCollection || "", possiblePath || "");
                    if (!doc) {
                        // Try fuzzy match by path ending
                        doc = db.prepare(`
              SELECT d.collection as collectionName, d.path, content.doc as body
              FROM documents d
              JOIN content ON content.hash = d.hash
              WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
              LIMIT 1
            `).get(possibleCollection || "", `%${possiblePath}`);
                    }
                    if (doc) {
                        virtualPath = buildVirtualPath(doc.collectionName, doc.path);
                        // Skip the filesystem path handling below
                    }
                }
            }
        }
        // If not found as collection/path, handle as filesystem paths
        if (!doc) {
            let fsPath = inputPath;
            // Expand ~ to home directory
            if (fsPath.startsWith('~/')) {
                fsPath = homedir() + fsPath.slice(1);
            }
            else if (!fsPath.startsWith('/')) {
                // Relative path - resolve from current directory
                fsPath = resolve(getPwd(), fsPath);
            }
            fsPath = getRealPath(fsPath);
            // Try to detect which collection contains this path
            const detected = detectCollectionFromPath(db, fsPath);
            if (detected) {
                // Found collection - query by collection name + relative path
                doc = db.prepare(`
          SELECT d.collection as collectionName, d.path, content.doc as body
          FROM documents d
          JOIN content ON content.hash = d.hash
          WHERE d.collection = ? AND d.path = ? AND d.active = 1
        `).get(detected.collectionName, detected.relativePath);
            }
            // Fuzzy match by filename (last component of path)
            if (!doc) {
                const filename = inputPath.split('/').pop() || inputPath;
                doc = db.prepare(`
          SELECT d.collection as collectionName, d.path, content.doc as body
          FROM documents d
          JOIN content ON content.hash = d.hash
          WHERE d.path LIKE ? AND d.active = 1
          LIMIT 1
        `).get(`%${filename}`);
            }
            if (doc) {
                virtualPath = buildVirtualPath(doc.collectionName, doc.path);
            }
            else {
                virtualPath = inputPath;
            }
        }
    }
    // Ensure doc is not null before proceeding
    if (!doc) {
        console.error(`Document not found: ${filename}`);
        closeDb();
        process.exit(1);
    }
    // Get context for this file
    const context = getContextForPath(db, doc.collectionName, doc.path);
    let output = doc.body;
    const startLine = fromLine || 1;
    // Apply line filtering if specified
    if (fromLine !== undefined || maxLines !== undefined) {
        const lines = output.split('\n');
        const start = startLine - 1; // Convert to 0-indexed
        const end = maxLines !== undefined ? start + maxLines : lines.length;
        output = lines.slice(start, end).join('\n');
    }
    // Add line numbers if requested
    if (lineNumbers) {
        output = addLineNumbers(output, startLine);
    }
    // Output context header if exists
    if (context) {
        console.log(`Folder Context: ${context}\n---\n`);
    }
    console.log(output);
    closeDb();
}
// Multi-get: fetch multiple documents by glob pattern or comma-separated list
function multiGet(pattern, maxLines, maxBytes = DEFAULT_MULTI_GET_MAX_BYTES, format = "cli") {
    const db = getDb();
    // Check if it's a comma-separated list or a glob pattern
    const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?') && !pattern.includes('{');
    let files;
    if (isCommaSeparated) {
        // Comma-separated list of files (can be virtual paths or relative paths)
        const names = pattern.split(',').map(s => s.trim()).filter(Boolean);
        files = [];
        for (const name of names) {
            let doc = null;
            // Handle virtual paths
            if (isVirtualPath(name)) {
                const parsed = parseVirtualPath(name);
                if (parsed) {
                    // Try exact match on collection + path
                    doc = db.prepare(`
            SELECT
              'qmd://' || d.collection || '/' || d.path as virtual_path,
              LENGTH(content.doc) as body_length,
              d.collection,
              d.path
            FROM documents d
            JOIN content ON content.hash = d.hash
            WHERE d.collection = ? AND d.path = ? AND d.active = 1
          `).get(parsed.collectionName, parsed.path);
                }
            }
            else {
                // Try exact match on path
                doc = db.prepare(`
          SELECT
            'qmd://' || d.collection || '/' || d.path as virtual_path,
            LENGTH(content.doc) as body_length,
            d.collection,
            d.path
          FROM documents d
          JOIN content ON content.hash = d.hash
          WHERE d.path = ? AND d.active = 1
          LIMIT 1
        `).get(name);
                // Try suffix match
                if (!doc) {
                    doc = db.prepare(`
            SELECT
              'qmd://' || d.collection || '/' || d.path as virtual_path,
              LENGTH(content.doc) as body_length,
              d.collection,
              d.path
            FROM documents d
            JOIN content ON content.hash = d.hash
            WHERE d.path LIKE ? AND d.active = 1
            LIMIT 1
          `).get(`%${name}`);
                }
            }
            if (doc) {
                files.push({
                    filepath: doc.virtual_path,
                    displayPath: doc.virtual_path,
                    bodyLength: doc.body_length,
                    collection: doc.collection,
                    path: doc.path
                });
            }
            else {
                console.error(`File not found: ${name}`);
            }
        }
    }
    else {
        // Glob pattern - matchFilesByGlob now returns virtual paths
        files = matchFilesByGlob(db, pattern).map(f => ({
            ...f,
            collection: undefined, // Will be fetched later if needed
            path: undefined
        }));
        if (files.length === 0) {
            console.error(`No files matched pattern: ${pattern}`);
            closeDb();
            process.exit(1);
        }
    }
    // Collect results for structured output
    const results = [];
    for (const file of files) {
        // Parse virtual path to get collection info if not already available
        let collection = file.collection;
        let path = file.path;
        if (!collection || !path) {
            const parsed = parseVirtualPath(file.filepath);
            if (parsed) {
                collection = parsed.collectionName;
                path = parsed.path;
            }
        }
        // Get context using collection-scoped function
        const context = collection && path ? getContextForPath(db, collection, path) : null;
        // Check size limit
        if (file.bodyLength > maxBytes) {
            results.push({
                file: file.filepath,
                displayPath: file.displayPath,
                title: file.displayPath.split('/').pop() || file.displayPath,
                body: "",
                context,
                skipped: true,
                skipReason: `File too large (${Math.round(file.bodyLength / 1024)}KB > ${Math.round(maxBytes / 1024)}KB). Use 'qmd get ${file.displayPath}' to retrieve.`,
            });
            continue;
        }
        // Fetch document content using collection and path
        if (!collection || !path)
            continue;
        const doc = db.prepare(`
      SELECT content.doc as body, d.title
      FROM documents d
      JOIN content ON content.hash = d.hash
      WHERE d.collection = ? AND d.path = ? AND d.active = 1
    `).get(collection, path);
        if (!doc)
            continue;
        let body = doc.body;
        // Apply line limit if specified
        if (maxLines !== undefined) {
            const lines = body.split('\n');
            body = lines.slice(0, maxLines).join('\n');
            if (lines.length > maxLines) {
                body += `\n\n[... truncated ${lines.length - maxLines} more lines]`;
            }
        }
        results.push({
            file: file.filepath,
            displayPath: file.displayPath,
            title: doc.title || file.displayPath.split('/').pop() || file.displayPath,
            body,
            context,
            skipped: false,
        });
    }
    closeDb();
    // Output based on format
    if (format === "json") {
        const output = results.map(r => ({
            file: r.displayPath,
            title: r.title,
            ...(r.context && { context: r.context }),
            ...(r.skipped ? { skipped: true, reason: r.skipReason } : { body: r.body }),
        }));
        console.log(JSON.stringify(output, null, 2));
    }
    else if (format === "csv") {
        const escapeField = (val) => {
            if (val === null || val === undefined)
                return "";
            const str = String(val);
            if (str.includes(",") || str.includes('"') || str.includes("\n")) {
                return `"${str.replace(/"/g, '""')}"`;
            }
            return str;
        };
        console.log("file,title,context,skipped,body");
        for (const r of results) {
            console.log([r.displayPath, r.title, r.context, r.skipped ? "true" : "false", r.skipped ? r.skipReason : r.body].map(escapeField).join(","));
        }
    }
    else if (format === "files") {
        for (const r of results) {
            const ctx = r.context ? `,"${r.context.replace(/"/g, '""')}"` : "";
            const status = r.skipped ? "[SKIPPED]" : "";
            console.log(`${r.displayPath}${ctx}${status ? `,${status}` : ""}`);
        }
    }
    else if (format === "md") {
        for (const r of results) {
            console.log(`## ${r.displayPath}\n`);
            if (r.title && r.title !== r.displayPath)
                console.log(`**Title:** ${r.title}\n`);
            if (r.context)
                console.log(`**Context:** ${r.context}\n`);
            if (r.skipped) {
                console.log(`> ${r.skipReason}\n`);
            }
            else {
                console.log("```");
                console.log(r.body);
                console.log("```\n");
            }
        }
    }
    else if (format === "xml") {
        console.log('<?xml version="1.0" encoding="UTF-8"?>');
        console.log("<documents>");
        for (const r of results) {
            console.log("  <document>");
            console.log(`    <file>${escapeXml(r.displayPath)}</file>`);
            console.log(`    <title>${escapeXml(r.title)}</title>`);
            if (r.context)
                console.log(`    <context>${escapeXml(r.context)}</context>`);
            if (r.skipped) {
                console.log(`    <skipped>true</skipped>`);
                console.log(`    <reason>${escapeXml(r.skipReason || "")}</reason>`);
            }
            else {
                console.log(`    <body>${escapeXml(r.body)}</body>`);
            }
            console.log("  </document>");
        }
        console.log("</documents>");
    }
    else {
        // CLI format (default)
        for (const r of results) {
            console.log(`\n${'='.repeat(60)}`);
            console.log(`File: ${r.displayPath}`);
            console.log(`${'='.repeat(60)}\n`);
            if (r.skipped) {
                console.log(`[SKIPPED: ${r.skipReason}]`);
                continue;
            }
            if (r.context) {
                console.log(`Folder Context: ${r.context}\n---\n`);
            }
            console.log(r.body);
        }
    }
}
// List files in virtual file tree
function listFiles(pathArg) {
    const db = getDb();
    if (!pathArg) {
        // No argument - list all collections
        const yamlCollections = yamlListCollections();
        if (yamlCollections.length === 0) {
            console.log("No collections found. Run 'qmd collection add .' to index files.");
            closeDb();
            return;
        }
        // Get file counts from database for each collection
        const collections = yamlCollections.map(coll => {
            const stats = db.prepare(`
        SELECT COUNT(*) as file_count
        FROM documents d
        WHERE d.collection = ? AND d.active = 1
      `).get(coll.name);
            return {
                name: coll.name,
                file_count: stats?.file_count || 0
            };
        });
        console.log(`${c.bold}Collections:${c.reset}\n`);
        for (const coll of collections) {
            console.log(`  ${c.dim}qmd://${c.reset}${c.cyan}${coll.name}/${c.reset}  ${c.dim}(${coll.file_count} files)${c.reset}`);
        }
        closeDb();
        return;
    }
    // Parse the path argument
    let collectionName;
    let pathPrefix = null;
    if (pathArg.startsWith('qmd://')) {
        // Virtual path format: qmd://collection/path
        const parsed = parseVirtualPath(pathArg);
        if (!parsed) {
            console.error(`Invalid virtual path: ${pathArg}`);
            closeDb();
            process.exit(1);
        }
        collectionName = parsed.collectionName;
        pathPrefix = parsed.path;
    }
    else {
        // Just collection name or collection/path
        const parts = pathArg.split('/');
        collectionName = parts[0] || '';
        if (parts.length > 1) {
            pathPrefix = parts.slice(1).join('/');
        }
    }
    // Get the collection
    const coll = getCollectionFromYaml(collectionName);
    if (!coll) {
        console.error(`Collection not found: ${collectionName}`);
        console.error(`Run 'qmd ls' to see available collections.`);
        closeDb();
        process.exit(1);
    }
    // List files in the collection with size and modification time
    let query;
    let params;
    if (pathPrefix) {
        // List files under a specific path
        query = `
      SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
      FROM documents d
      JOIN content ct ON d.hash = ct.hash
      WHERE d.collection = ? AND d.path LIKE ? AND d.active = 1
      ORDER BY d.path
    `;
        params = [coll.name, `${pathPrefix}%`];
    }
    else {
        // List all files in the collection
        query = `
      SELECT d.path, d.title, d.modified_at, LENGTH(ct.doc) as size
      FROM documents d
      JOIN content ct ON d.hash = ct.hash
      WHERE d.collection = ? AND d.active = 1
      ORDER BY d.path
    `;
        params = [coll.name];
    }
    const files = db.prepare(query).all(...params);
    if (files.length === 0) {
        if (pathPrefix) {
            console.log(`No files found under qmd://${collectionName}/${pathPrefix}`);
        }
        else {
            console.log(`No files found in collection: ${collectionName}`);
        }
        closeDb();
        return;
    }
    // Calculate max widths for alignment
    const maxSize = Math.max(...files.map(f => formatBytes(f.size).length));
    // Output in ls -l style
    for (const file of files) {
        const sizeStr = formatBytes(file.size).padStart(maxSize);
        const date = new Date(file.modified_at);
        const timeStr = formatLsTime(date);
        // Dim the qmd:// prefix, highlight the filename
        console.log(`${sizeStr}  ${timeStr}  ${c.dim}qmd://${collectionName}/${c.reset}${c.cyan}${file.path}${c.reset}`);
    }
    closeDb();
}
// Format date/time like ls -l
function formatLsTime(date) {
    const now = new Date();
    const sixMonthsAgo = new Date(now.getTime() - 6 * 30 * 24 * 60 * 60 * 1000);
    const months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec'];
    const month = months[date.getMonth()];
    const day = date.getDate().toString().padStart(2, ' ');
    // If file is older than 6 months, show year instead of time
    if (date < sixMonthsAgo) {
        const year = date.getFullYear();
        return `${month} ${day}  ${year}`;
    }
    else {
        const hours = date.getHours().toString().padStart(2, '0');
        const minutes = date.getMinutes().toString().padStart(2, '0');
        return `${month} ${day} ${hours}:${minutes}`;
    }
}
// Collection management commands
function collectionList() {
    const db = getDb();
    const collections = listCollections(db);
    if (collections.length === 0) {
        console.log("No collections found. Run 'qmd collection add .' to create one.");
        closeDb();
        return;
    }
    console.log(`${c.bold}Collections (${collections.length}):${c.reset}\n`);
    for (const coll of collections) {
        const updatedAt = coll.last_modified ? new Date(coll.last_modified) : new Date();
        const timeAgo = formatTimeAgo(updatedAt);
        // Get YAML config to check includeByDefault
        const yamlColl = getCollectionFromYaml(coll.name);
        const excluded = yamlColl?.includeByDefault === false;
        const excludeTag = excluded ? ` ${c.yellow}[excluded]${c.reset}` : '';
        console.log(`${c.cyan}${coll.name}${c.reset} ${c.dim}(qmd://${coll.name}/)${c.reset}${excludeTag}`);
        console.log(`  ${c.dim}Pattern:${c.reset}  ${coll.glob_pattern}`);
        if (yamlColl?.ignore?.length) {
            console.log(`  ${c.dim}Ignore:${c.reset}   ${yamlColl.ignore.join(', ')}`);
        }
        console.log(`  ${c.dim}Files:${c.reset}    ${coll.active_count}`);
        console.log(`  ${c.dim}Updated:${c.reset}  ${timeAgo}`);
        console.log();
    }
    closeDb();
}
async function collectionAdd(pwd, globPattern, name) {
    // If name not provided, generate from pwd basename
    let collName = name;
    if (!collName) {
        const parts = pwd.split('/').filter(Boolean);
        collName = parts[parts.length - 1] || 'root';
    }
    // Check if collection with this name already exists in YAML
    const existing = getCollectionFromYaml(collName);
    if (existing) {
        console.error(`${c.yellow}Collection '${collName}' already exists.${c.reset}`);
        console.error(`Use a different name with --name <name>`);
        process.exit(1);
    }
    // Check if a collection with this pwd+glob already exists in YAML
    const allCollections = yamlListCollections();
    const existingPwdGlob = allCollections.find(c => c.path === pwd && c.pattern === globPattern);
    if (existingPwdGlob) {
        console.error(`${c.yellow}A collection already exists for this path and pattern:${c.reset}`);
        console.error(`  Name: ${existingPwdGlob.name} (qmd://${existingPwdGlob.name}/)`);
        console.error(`  Pattern: ${globPattern}`);
        console.error(`\nUse 'qmd update' to re-index it, or remove it first with 'qmd collection remove ${existingPwdGlob.name}'`);
        process.exit(1);
    }
    // Add to YAML config + sync to SQLite
    const { addCollection } = await import("../collections.js");
    addCollection(collName, pwd, globPattern);
    resyncConfig();
    // Create the collection and index files
    console.log(`Creating collection '${collName}'...`);
    const newColl = getCollectionFromYaml(collName);
    await indexFiles(pwd, globPattern, collName, false, newColl?.ignore);
    console.log(`${c.green}✓${c.reset} Collection '${collName}' created successfully`);
}
function collectionRemove(name) {
    // Check if collection exists in YAML
    const coll = getCollectionFromYaml(name);
    if (!coll) {
        console.error(`${c.yellow}Collection not found: ${name}${c.reset}`);
        console.error(`Run 'qmd collection list' to see available collections.`);
        process.exit(1);
    }
    const db = getDb();
    const result = removeCollection(db, name);
    // Also remove from YAML config
    yamlRemoveCollectionFn(name);
    closeDb();
    console.log(`${c.green}✓${c.reset} Removed collection '${name}'`);
    console.log(`  Deleted ${result.deletedDocs} documents`);
    if (result.cleanedHashes > 0) {
        console.log(`  Cleaned up ${result.cleanedHashes} orphaned content hashes`);
    }
}
function collectionRename(oldName, newName) {
    // Check if old collection exists in YAML
    const coll = getCollectionFromYaml(oldName);
    if (!coll) {
        console.error(`${c.yellow}Collection not found: ${oldName}${c.reset}`);
        console.error(`Run 'qmd collection list' to see available collections.`);
        process.exit(1);
    }
    // Check if new name already exists in YAML
    const existing = getCollectionFromYaml(newName);
    if (existing) {
        console.error(`${c.yellow}Collection name already exists: ${newName}${c.reset}`);
        console.error(`Choose a different name or remove the existing collection first.`);
        process.exit(1);
    }
    const db = getDb();
    renameCollection(db, oldName, newName);
    // Also rename in YAML config
    yamlRenameCollectionFn(oldName, newName);
    closeDb();
    console.log(`${c.green}✓${c.reset} Renamed collection '${oldName}' to '${newName}'`);
    console.log(`  Virtual paths updated: ${c.cyan}qmd://${oldName}/${c.reset} → ${c.cyan}qmd://${newName}/${c.reset}`);
}
async function indexFiles(pwd, globPattern = DEFAULT_GLOB, collectionName, suppressEmbedNotice = false, ignorePatterns) {
    const db = getDb();
    const resolvedPwd = pwd || getPwd();
    const now = new Date().toISOString();
    const excludeDirs = ["node_modules", ".git", ".cache", "vendor", "dist", "build"];
    // Clear Ollama cache on index
    clearCache(db);
    // Collection name must be provided (from YAML)
    if (!collectionName) {
        throw new Error("Collection name is required. Collections must be defined in ~/.config/qmd/index.yml");
    }
    console.log(`Collection: ${resolvedPwd} (${globPattern})`);
    progress.indeterminate();
    const allIgnore = [
        ...excludeDirs.map(d => `**/${d}/**`),
        ...(ignorePatterns || []),
    ];
    const allFiles = await fastGlob(globPattern, {
        cwd: resolvedPwd,
        onlyFiles: true,
        followSymbolicLinks: false,
        dot: false,
        ignore: allIgnore,
    });
    // Filter hidden files/folders (dot: false handles top-level but not nested)
    const files = allFiles.filter(file => {
        const parts = file.split("/");
        return !parts.some(part => part.startsWith("."));
    });
    const total = files.length;
    const hasNoFiles = total === 0;
    if (hasNoFiles) {
        progress.clear();
        console.log("No files found matching pattern.");
        // Continue so the deactivation pass can mark previously indexed docs as inactive.
    }
    let indexed = 0, updated = 0, unchanged = 0, processed = 0;
    const seenPaths = new Set();
    const startTime = Date.now();
    for (const relativeFile of files) {
        const filepath = getRealPath(resolve(resolvedPwd, relativeFile));
        const path = handelize(relativeFile); // Normalize path for token-friendliness
        seenPaths.add(path);
        let content;
        try {
            content = readFileSync(filepath, "utf-8");
        }
        catch (err) {
            // Skip files that can't be read (e.g. iCloud evicted files returning EAGAIN)
            processed++;
            progress.set((processed / total) * 100);
            continue;
        }
        // Skip empty files - nothing useful to index
        if (!content.trim()) {
            processed++;
            continue;
        }
        const hash = await hashContent(content);
        const title = extractTitle(content, relativeFile);
        // Check if document exists in this collection with this path
        const existing = findActiveDocument(db, collectionName, path);
        if (existing) {
            if (existing.hash === hash) {
                // Hash unchanged, but check if title needs updating
                if (existing.title !== title) {
                    updateDocumentTitle(db, existing.id, title, now);
                    updated++;
                }
                else {
                    unchanged++;
                }
            }
            else {
                // Content changed - insert new content hash and update document
                insertContent(db, hash, content, now);
                const stat = statSync(filepath);
                updateDocument(db, existing.id, title, hash, stat ? new Date(stat.mtime).toISOString() : now);
                updated++;
            }
        }
        else {
            // New document - insert content and document
            indexed++;
            insertContent(db, hash, content, now);
            const stat = statSync(filepath);
            insertDocument(db, collectionName, path, title, hash, stat ? new Date(stat.birthtime).toISOString() : now, stat ? new Date(stat.mtime).toISOString() : now);
        }
        processed++;
        progress.set((processed / total) * 100);
        const elapsed = (Date.now() - startTime) / 1000;
        const rate = processed / elapsed;
        const remaining = (total - processed) / rate;
        const eta = processed > 2 ? ` ETA: ${formatETA(remaining)}` : "";
        if (isTTY)
            process.stderr.write(`\rIndexing: ${processed}/${total}${eta}        `);
    }
    // Deactivate documents in this collection that no longer exist
    const allActive = getActiveDocumentPaths(db, collectionName);
    let removed = 0;
    for (const path of allActive) {
        if (!seenPaths.has(path)) {
            deactivateDocument(db, collectionName, path);
            removed++;
        }
    }
    // Clean up orphaned content hashes (content not referenced by any document)
    const orphanedContent = cleanupOrphanedContent(db);
    // Check if vector index needs updating
    const needsEmbedding = getHashesNeedingEmbedding(db);
    progress.clear();
    console.log(`\nIndexed: ${indexed} new, ${updated} updated, ${unchanged} unchanged, ${removed} removed`);
    if (orphanedContent > 0) {
        console.log(`Cleaned up ${orphanedContent} orphaned content hash(es)`);
    }
    if (needsEmbedding > 0 && !suppressEmbedNotice) {
        console.log(`\nRun 'qmd embed' to update embeddings (${needsEmbedding} unique hashes need vectors)`);
    }
    closeDb();
}
function renderProgressBar(percent, width = 30) {
    const filled = Math.round((percent / 100) * width);
    const empty = width - filled;
    const bar = "█".repeat(filled) + "░".repeat(empty);
    return bar;
}
function parseEmbedBatchOption(name, value) {
    if (value === undefined)
        return undefined;
    const parsed = Number(value);
    if (!Number.isInteger(parsed) || parsed < 1) {
        throw new Error(`${name} must be a positive integer`);
    }
    return parsed;
}
function parseChunkStrategy(value) {
    if (value === undefined)
        return undefined;
    const s = String(value);
    if (s === "auto" || s === "regex" || s === "function")
        return s;
    throw new Error(`--chunk-strategy must be "auto", "regex", or "function" (got "${s}")`);
}
function parseProviderKind(value) {
    if (value === undefined)
        return undefined;
    const s = String(value).toLowerCase();
    if (s === "local" || s === "openai")
        return s;
    throw new Error(`--provider must be "local" or "openai" (got "${s}")`);
}
function parseOptionalPositiveInt(name, value) {
    if (value === undefined)
        return undefined;
    const parsed = Number(value);
    if (!Number.isInteger(parsed) || parsed < 1) {
        throw new Error(`${name} must be a positive integer`);
    }
    return parsed;
}
/**
 * Translate `cli.values` into `CreateEmbeddingProviderOptions`. CLI flags
 * win over env vars (the factory itself reads env when these are unset).
 */
function buildProviderOpts(values, providerCliKind) {
    const endpoint = optionalString(values["embed-endpoint"]);
    const apiKey = optionalString(values["embed-api-key"]);
    const modelId = optionalString(values["embed-model-id"]);
    const upstreamModel = optionalString(values["embed-upstream-model"]);
    const batchSize = parseOptionalPositiveInt("--embed-batch-size", values["embed-batch-size"]);
    const timeoutMs = parseOptionalPositiveInt("--embed-timeout-ms", values["embed-timeout-ms"]);
    // Only build the openai overrides object if the user supplied flags
    const openai = endpoint || apiKey || modelId || upstreamModel || batchSize !== undefined || timeoutMs !== undefined
        ? {
            ...(endpoint !== undefined ? { endpoint } : {}),
            ...(apiKey !== undefined ? { apiKey } : {}),
            ...(modelId !== undefined ? { modelId } : {}),
            ...(upstreamModel !== undefined ? { upstreamModel } : {}),
            ...(batchSize !== undefined ? { batchSize } : {}),
            ...(timeoutMs !== undefined ? { timeoutMs } : {}),
        }
        : undefined;
    // CLI flag for auto-fallback wrapping (only meaningful when kind === openai)
    const autoFallback = values["embed-auto-fallback"] === true ? true : undefined;
    return {
        ...(providerCliKind ? { kind: providerCliKind } : {}),
        ...(openai ? { openai } : {}),
        ...(autoFallback !== undefined ? { autoFallback } : {}),
    };
}
function optionalString(v) {
    if (v === undefined || v === null)
        return undefined;
    const s = String(v);
    return s === "" ? undefined : s;
}
async function vectorIndex(model = DEFAULT_EMBED_MODEL_URI, force = false, batchOptions) {
    const storeInstance = getStore();
    const db = storeInstance.db;
    if (force) {
        console.log(`${c.yellow}Force re-indexing: clearing all vectors...${c.reset}`);
    }
    // Check if there's work to do before starting
    const hashesToEmbed = getHashesNeedingEmbedding(db);
    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`);
    if (batchOptions?.embedProvider) {
        const kind = batchOptions.embedProvider.kind;
        const providerModel = batchOptions.embedProvider.getModelId();
        console.log(`${c.dim}Provider: ${kind} (model id "${providerModel}")${c.reset}\n`);
    }
    else if (batchOptions?.providerKind) {
        console.log(`${c.dim}Provider: ${batchOptions.providerKind}${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,
        maxDocsPerBatch: batchOptions?.maxDocsPerBatch,
        maxBatchBytes: batchOptions?.maxBatchBytes,
        chunkStrategy: batchOptions?.chunkStrategy,
        embedProvider: batchOptions?.embedProvider,
        onProgress: (info) => {
            if (info.totalBytes === 0)
                return;
            const percent = (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 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${c.reset}` : "";
            if (isTTY)
                process.stderr.write(`\r${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}   `);
        },
    });
    progress.clear();
    cursor.show();
    const totalTimeSec = result.durationMs / 1000;
    if (result.chunksEmbedded === 0 && result.docsProcessed === 0) {
        console.log(`${c.green}✓ No non-empty documents to embed.${c.reset}`);
    }
    else {
        console.log(`\r${c.green}${renderProgressBar(100)}${c.reset} ${c.bold}100%${c.reset}                                    `);
        console.log(`\n${c.green}✓ Done!${c.reset} Embedded ${c.bold}${result.chunksEmbedded}${c.reset} chunks from ${c.bold}${result.docsProcessed}${c.reset} documents in ${c.bold}${formatETA(totalTimeSec)}${c.reset}`);
        if (result.errors > 0) {
            console.log(`${c.yellow}⚠ ${result.errors} chunks failed${c.reset}`);
        }
    }
    closeDb();
}
// Sanitize a term for FTS5: remove punctuation except apostrophes
function sanitizeFTS5Term(term) {
    // Remove all non-alphanumeric except apostrophes (for contractions like "don't")
    return term.replace(/[^\w']/g, '').trim();
}
// Build FTS5 query: phrase-aware with fallback to individual terms
function buildFTS5Query(query) {
    // Sanitize the full query for phrase matching
    const sanitizedQuery = query.replace(/[^\w\s']/g, '').trim();
    const terms = query
        .split(/\s+/)
        .map(sanitizeFTS5Term)
        .filter(term => term.length >= 2); // Skip single chars and empty
    if (terms.length === 0)
        return "";
    if (terms.length === 1)
        return `"${terms[0].replace(/"/g, '""')}"`;
    // Strategy: exact phrase OR proximity match OR individual terms
    // Exact phrase matches rank highest, then close proximity, then any term
    const phrase = `"${sanitizedQuery.replace(/"/g, '""')}"`;
    const quotedTerms = terms.map(t => `"${t.replace(/"/g, '""')}"`);
    // FTS5 NEAR syntax: NEAR(term1 term2, distance)
    const nearPhrase = `NEAR(${quotedTerms.join(' ')}, 10)`;
    const orTerms = quotedTerms.join(' OR ');
    // Exact phrase > proximity > any term
    return `(${phrase}) OR (${nearPhrase}) OR (${orTerms})`;
}
// Normalize BM25 score to 0-1 range using sigmoid
function normalizeBM25(score) {
    // BM25 scores are negative in SQLite (lower = better)
    // Typical range: -15 (excellent) to -2 (weak match)
    // Map to 0-1 where higher is better
    const absScore = Math.abs(score);
    // Sigmoid-ish normalization: maps ~2-15 range to ~0.1-0.95
    return 1 / (1 + Math.exp(-(absScore - 5) / 3));
}
// Highlight query terms in text (skip short words < 3 chars)
function highlightTerms(text, query) {
    if (!useColor)
        return text;
    const terms = query.toLowerCase().split(/\s+/).filter(t => t.length >= 3);
    let result = text;
    for (const term of terms) {
        const regex = new RegExp(`(${term.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')})`, 'gi');
        result = result.replace(regex, `${c.yellow}${c.bold}$1${c.reset}`);
    }
    return result;
}
// Format score with color based on value
function formatScore(score) {
    const pct = (score * 100).toFixed(0).padStart(3);
    if (!useColor)
        return `${pct}%`;
    if (score >= 0.7)
        return `${c.green}${pct}%${c.reset}`;
    if (score >= 0.4)
        return `${c.yellow}${pct}%${c.reset}`;
    return `${c.dim}${pct}%${c.reset}`;
}
function formatExplainNumber(value) {
    return value.toFixed(4);
}
// Shorten directory path for display - relative to $HOME (used for context paths, not documents)
function shortPath(dirpath) {
    const home = homedir();
    if (dirpath.startsWith(home)) {
        return '~' + dirpath.slice(home.length);
    }
    return dirpath;
}
// Emit format-safe empty output for search commands.
function printEmptySearchResults(format, reason = "no_results") {
    if (format === "json") {
        console.log("[]");
        return;
    }
    if (format === "csv") {
        console.log("docid,score,file,title,context,line,snippet");
        return;
    }
    if (format === "xml") {
        console.log("<results></results>");
        return;
    }
    if (format === "md" || format === "files") {
        return;
    }
    if (reason === "min_score") {
        console.log("No results found above minimum score threshold.");
        return;
    }
    console.log("No results found.");
}
const DEFAULT_EDITOR_URI_TEMPLATE = "vscode://file/{path}:{line}:{col}";
function encodePathForEditorUri(absolutePath) {
    return encodeURI(absolutePath)
        .replace(/\?/g, "%3F")
        .replace(/#/g, "%23");
}
function getEditorUriTemplate() {
    const envTemplate = process.env.QMD_EDITOR_URI?.trim();
    if (envTemplate)
        return envTemplate;
    try {
        const config = loadConfig();
        const configTemplate = (config.editor_uri
            || config.editor_uri_template
            || config.editorUri
            || (typeof config["editor-uri"] === "string" ? config["editor-uri"] : undefined))?.trim();
        if (configTemplate)
            return configTemplate;
    }
    catch {
        // Ignore config parsing issues and use default template.
    }
    return DEFAULT_EDITOR_URI_TEMPLATE;
}
export function buildEditorUri(template, absolutePath, line, col) {
    const safeLine = Number.isFinite(line) && line > 0 ? Math.floor(line) : 1;
    const safeCol = Number.isFinite(col) && col > 0 ? Math.floor(col) : 1;
    const encodedPath = encodePathForEditorUri(absolutePath);
    return template
        .replace(/\{path\}/g, encodedPath)
        .replace(/\{line\}/g, String(safeLine))
        .replace(/\{col\}/g, String(safeCol))
        .replace(/\{column\}/g, String(safeCol));
}
export function termLink(text, url, isTTY = !!process.stdout.isTTY) {
    if (!isTTY)
        return text;
    return `\x1b]8;;${url}\x07${text}\x1b]8;;\x07`;
}
function outputResults(results, query, opts) {
    const filtered = results.filter(r => r.score >= opts.minScore).slice(0, opts.limit);
    if (filtered.length === 0) {
        printEmptySearchResults(opts.format, "min_score");
        return;
    }
    // Helper to create qmd:// URI from displayPath
    const toQmdPath = (displayPath) => `qmd://${displayPath}`;
    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);
            let body = opts.full ? row.body : undefined;
            let snippet = !opts.full ? extractSnippet(row.body, query, 300, row.chunkPos, undefined, opts.intent).snippet : undefined;
            if (opts.lineNumbers) {
                if (body)
                    body = addLineNumbers(body);
                if (snippet)
                    snippet = addLineNumbers(snippet);
            }
            return {
                ...(docid && { docid: `#${docid}` }),
                score: Math.round(row.score * 100) / 100,
                file: toQmdPath(row.displayPath),
                title: row.title,
                ...(row.context && { context: row.context }),
                ...(body && { body }),
                ...(snippet && { snippet }),
                ...(opts.explain && row.explain && { explain: row.explain }),
            };
        });
        console.log(JSON.stringify(output, null, 2));
    }
    else if (opts.format === "files") {
        // Simple docid,score,filepath,context output
        for (const row of filtered) {
            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
            const ctx = row.context ? `,"${row.context.replace(/"/g, '""')}"` : "";
            console.log(`#${docid},${row.score.toFixed(2)},${toQmdPath(row.displayPath)}${ctx}`);
        }
    }
    else if (opts.format === "cli") {
        const editorUriTemplate = getEditorUriTemplate();
        const linkDb = getDb();
        for (let i = 0; i < filtered.length; i++) {
            const row = filtered[i];
            if (!row)
                continue;
            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, undefined, opts.intent);
            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);
            // Line 1: filepath with docid
            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}${c.reset}` : "";
            if (process.stdout.isTTY && absolutePath && parsed?.path) {
                const linkLine = hasMatch ? line : 1;
                const linkTarget = buildEditorUri(editorUriTemplate, absolutePath, linkLine, 1);
                const clickable = termLink(`${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}`);
            }
            // Line 3: Context (if available)
            if (row.context) {
                console.log(`${c.dim}Context: ${row.context}${c.reset}`);
            }
            // Line 4: Score
            const score = formatScore(row.score);
            console.log(`Score: ${c.bold}${score}${c.reset}`);
            if (opts.explain && row.explain) {
                const explain = row.explain;
                const ftsScores = explain.ftsScores.length > 0
                    ? explain.ftsScores.map(formatExplainNumber).join(", ")
                    : "none";
                const vecScores = explain.vectorScores.length > 0
                    ? explain.vectorScores.map(formatExplainNumber).join(", ")
                    : "none";
                const contribSummary = explain.rrf.contributions
                    .slice()
                    .sort((a, b) => b.rrfContribution - a.rrfContribution)
                    .slice(0, 3)
                    .map(c => `${c.source}/${c.queryType}#${c.rank}:${formatExplainNumber(c.rrfContribution)}`)
                    .join(" | ");
                console.log(`${c.dim}Explain: fts=[${ftsScores}] vec=[${vecScores}]${c.reset}`);
                console.log(`${c.dim}  RRF: total=${formatExplainNumber(explain.rrf.totalScore)} base=${formatExplainNumber(explain.rrf.baseScore)} bonus=${formatExplainNumber(explain.rrf.topRankBonus)} rank=${explain.rrf.rank}${c.reset}`);
                console.log(`${c.dim}  Blend: ${Math.round(explain.rrf.weight * 100)}%*${formatExplainNumber(explain.rrf.positionScore)} + ${Math.round((1 - explain.rrf.weight) * 100)}%*${formatExplainNumber(explain.rerankScore)} = ${formatExplainNumber(explain.blendedScore)}${c.reset}`);
                if (contribSummary.length > 0) {
                    console.log(`${c.dim}  Top RRF contributions: ${contribSummary}${c.reset}`);
                }
            }
            console.log();
            // Snippet with highlighting (diff-style header included)
            let displaySnippet = opts.lineNumbers ? addLineNumbers(snippet, line) : snippet;
            const highlighted = highlightTerms(displaySnippet, query);
            console.log(highlighted);
            // Double empty line between results
            if (i < filtered.length - 1)
                console.log('\n');
        }
    }
    else if (opts.format === "md") {
        for (let i = 0; i < filtered.length; i++) {
            const row = filtered[i];
            if (!row)
                continue;
            const 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;
            if (opts.lineNumbers) {
                content = addLineNumbers(content);
            }
            const docidLine = docid ? `**docid:** \`#${docid}\`\n` : "";
            const contextLine = row.context ? `**context:** ${row.context}\n` : "";
            console.log(`---\n# ${heading}\n${docidLine}${contextLine}\n${content}\n`);
        }
    }
    else if (opts.format === "xml") {
        for (const row of filtered) {
            const titleAttr = row.title ? ` title="${row.title.replace(/"/g, '&quot;')}"` : "";
            const contextAttr = row.context ? ` context="${row.context.replace(/"/g, '&quot;')}"` : "";
            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
            let content = opts.full ? row.body : extractSnippet(row.body, query, 500, row.chunkPos, undefined, opts.intent).snippet;
            if (opts.lineNumbers) {
                content = addLineNumbers(content);
            }
            console.log(`<file docid="#${docid}" name="${toQmdPath(row.displayPath)}"${titleAttr}${contextAttr}>\n${content}\n</file>\n`);
        }
    }
    else {
        // CSV format
        console.log("docid,score,file,title,context,line,snippet");
        for (const row of filtered) {
            const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos, undefined, opts.intent);
            let content = opts.full ? row.body : snippet;
            if (opts.lineNumbers) {
                content = addLineNumbers(content, line);
            }
            const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
            const snippetText = content || "";
            console.log(`#${docid},${row.score.toFixed(4)},${escapeCSV(toQmdPath(row.displayPath))},${escapeCSV(row.title || "")},${escapeCSV(row.context || "")},${line},${escapeCSV(snippetText)}`);
        }
    }
}
// Resolve -c collection filter: supports single string, array, or undefined.
// Returns validated collection names (exits on unknown collection).
function resolveCollectionFilter(raw, useDefaults = false) {
    // If no filter specified and useDefaults is true, use default collections
    if (!raw && useDefaults) {
        return getDefaultCollectionNames();
    }
    if (!raw)
        return [];
    const names = Array.isArray(raw) ? raw : [raw];
    const validated = [];
    for (const name of names) {
        const coll = getCollectionFromYaml(name);
        if (!coll) {
            console.error(`Collection not found: ${name}`);
            closeDb();
            process.exit(1);
        }
        validated.push(name);
    }
    return validated;
}
// Post-filter results to only include files from specified collections.
function filterByCollections(results, collectionNames) {
    if (collectionNames.length <= 1)
        return results;
    const prefixes = collectionNames.map(n => `qmd://${n}/`);
    return results.filter(r => {
        const path = r.filepath || r.file || '';
        return prefixes.some(p => path.startsWith(p));
    });
}
function parseStructuredQuery(query) {
    const rawLines = query.split('\n').map((line, idx) => ({
        raw: line,
        trimmed: line.trim(),
        number: idx + 1,
    })).filter(line => line.trimmed.length > 0);
    if (rawLines.length === 0)
        return null;
    const prefixRe = /^(lex|vec|hyde):\s*/i;
    const expandRe = /^expand:\s*/i;
    const intentRe = /^intent:\s*/i;
    const typed = [];
    let intent;
    for (const line of rawLines) {
        if (expandRe.test(line.trimmed)) {
            if (rawLines.length > 1) {
                throw new Error(`Line ${line.number} starts with expand:, but query documents cannot mix expand with typed lines. Submit a single expand query instead.`);
            }
            const text = line.trimmed.replace(expandRe, '').trim();
            if (!text) {
                throw new Error('expand: query must include text.');
            }
            return null; // treat as standalone expand query
        }
        // Parse intent: lines
        if (intentRe.test(line.trimmed)) {
            if (intent !== undefined) {
                throw new Error(`Line ${line.number}: only one intent: line is allowed per query document.`);
            }
            const text = line.trimmed.replace(intentRe, '').trim();
            if (!text) {
                throw new Error(`Line ${line.number}: intent: must include text.`);
            }
            intent = text;
            continue;
        }
        const match = line.trimmed.match(prefixRe);
        if (match) {
            const type = match[1].toLowerCase();
            const text = line.trimmed.slice(match[0].length).trim();
            if (!text) {
                throw new Error(`Line ${line.number} (${type}:) must include text.`);
            }
            if (/\r|\n/.test(text)) {
                throw new Error(`Line ${line.number} (${type}:) contains a newline. Keep each query on a single line.`);
            }
            typed.push({ type, query: text, line: line.number });
            continue;
        }
        if (rawLines.length === 1) {
            // Single plain line -> implicit expand
            return null;
        }
        throw new Error(`Line ${line.number} is missing a lex:/vec:/hyde:/intent: prefix. Each line in a query document must start with one.`);
    }
    // intent: alone is not a valid query — must have at least one search
    if (intent && typed.length === 0) {
        throw new Error('intent: cannot appear alone. Add at least one lex:, vec:, or hyde: line.');
    }
    return typed.length > 0 ? { searches: typed, intent } : null;
}
function search(query, opts) {
    const db = getDb();
    // Validate collection filter (supports multiple -c flags)
    // Use default collections if none specified
    const collectionNames = resolveCollectionFilter(opts.collection, true);
    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
    // Use large limit for --all, otherwise fetch more than needed and let outputResults filter
    const fetchLimit = opts.all ? 100000 : Math.max(50, opts.limit * 2);
    const results = filterByCollections(searchFTS(db, query, fetchLimit, singleCollection), collectionNames);
    // Add context to results
    const resultsWithContext = results.map(r => ({
        file: r.filepath,
        displayPath: r.displayPath,
        title: r.title,
        body: r.body || "",
        score: r.score,
        context: getContextForFile(db, r.filepath),
        hash: r.hash,
        docid: r.docid,
    }));
    closeDb();
    if (resultsWithContext.length === 0) {
        printEmptySearchResults(opts.format);
        return;
    }
    outputResults(resultsWithContext, query, opts);
}
// Log query expansion as a tree to stderr (CLI progress feedback)
function logExpansionTree(originalQuery, expanded) {
    const lines = [];
    lines.push(`${c.dim}├─ ${originalQuery}${c.reset}`);
    for (const q of expanded) {
        let preview = q.query.replace(/\n/g, ' ');
        if (preview.length > 72)
            preview = preview.substring(0, 69) + '...';
        lines.push(`${c.dim}├─ ${q.type}: ${preview}${c.reset}`);
    }
    if (lines.length > 0) {
        lines[lines.length - 1] = lines[lines.length - 1].replace('├─', '└─');
    }
    for (const line of lines)
        process.stderr.write(line + '\n');
}
async function vectorSearch(query, opts, _model = DEFAULT_EMBED_MODEL) {
    const store = getStore();
    // Validate collection filter (supports multiple -c flags)
    // Use default collections if none specified
    const collectionNames = resolveCollectionFilter(opts.collection, true);
    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
    checkIndexHealth(store.db);
    await withLLMSession(async () => {
        let results = await vectorSearchQuery(store, query, {
            collection: singleCollection,
            limit: opts.all ? 500 : (opts.limit || 10),
            minScore: opts.minScore || 0.3,
            intent: opts.intent,
            hooks: {
                onExpand: (original, expanded) => {
                    logExpansionTree(original, expanded);
                    process.stderr.write(`${c.dim}Searching ${expanded.length + 1} vector queries...${c.reset}\n`);
                },
            },
        });
        // Post-filter for multi-collection
        if (collectionNames.length > 1) {
            results = results.filter(r => {
                const prefixes = collectionNames.map(n => `qmd://${n}/`);
                return prefixes.some(p => r.file.startsWith(p));
            });
        }
        closeDb();
        if (results.length === 0) {
            printEmptySearchResults(opts.format);
            return;
        }
        outputResults(results.map(r => ({
            file: r.file,
            displayPath: r.displayPath,
            title: r.title,
            body: r.body,
            score: r.score,
            context: r.context,
            docid: r.docid,
        })), query, { ...opts, limit: results.length });
    }, { maxDuration: 10 * 60 * 1000, name: 'vectorSearch' });
}
async function querySearch(query, opts, _embedModel = DEFAULT_EMBED_MODEL, _rerankModel = DEFAULT_RERANK_MODEL) {
    const store = getStore();
    // Validate collection filter (supports multiple -c flags)
    // Use default collections if none specified
    const collectionNames = resolveCollectionFilter(opts.collection, true);
    const singleCollection = collectionNames.length === 1 ? collectionNames[0] : undefined;
    checkIndexHealth(store.db);
    // Check for structured query syntax (lex:/vec:/hyde:/intent: prefixes)
    const parsed = parseStructuredQuery(query);
    // Intent can come from --intent flag or from intent: line in query document
    const intent = opts.intent || parsed?.intent;
    await withLLMSession(async () => {
        let results;
        if (parsed) {
            const structuredQueries = parsed.searches;
            // Structured search — user provided their own query expansions
            const typeLabels = structuredQueries.map(s => s.type).join('+');
            process.stderr.write(`${c.dim}Structured search: ${structuredQueries.length} queries (${typeLabels})${c.reset}\n`);
            if (intent) {
                process.stderr.write(`${c.dim}├─ intent: ${intent}${c.reset}\n`);
            }
            // Log each sub-query
            for (const s of structuredQueries) {
                let preview = s.query.replace(/\n/g, ' ');
                if (preview.length > 72)
                    preview = preview.substring(0, 69) + '...';
                process.stderr.write(`${c.dim}├─ ${s.type}: ${preview}${c.reset}\n`);
            }
            process.stderr.write(`${c.dim}└─ Searching...${c.reset}\n`);
            results = await structuredSearch(store, structuredQueries, {
                collections: singleCollection ? [singleCollection] : undefined,
                limit: opts.all ? 500 : (opts.limit || 10),
                minScore: opts.minScore || 0,
                candidateLimit: opts.candidateLimit,
                skipRerank: opts.skipRerank,
                explain: !!opts.explain,
                intent,
                chunkStrategy: opts.chunkStrategy,
                hooks: {
                    onEmbedStart: (count) => {
                        process.stderr.write(`${c.dim}Embedding ${count} ${count === 1 ? 'query' : 'queries'}...${c.reset}`);
                    },
                    onEmbedDone: (ms) => {
                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
                    },
                    onRerankStart: (chunkCount) => {
                        process.stderr.write(`${c.dim}Reranking ${chunkCount} chunks...${c.reset}`);
                        progress.indeterminate();
                    },
                    onRerankDone: (ms) => {
                        progress.clear();
                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
                    },
                },
            });
        }
        else {
            // Standard hybrid query with automatic expansion
            results = await hybridQuery(store, query, {
                collection: singleCollection,
                limit: opts.all ? 500 : (opts.limit || 10),
                minScore: opts.minScore || 0,
                candidateLimit: opts.candidateLimit,
                skipRerank: opts.skipRerank,
                explain: !!opts.explain,
                intent,
                chunkStrategy: opts.chunkStrategy,
                hooks: {
                    onStrongSignal: (score) => {
                        process.stderr.write(`${c.dim}Strong BM25 signal (${score.toFixed(2)}) — skipping expansion${c.reset}\n`);
                    },
                    onExpandStart: () => {
                        process.stderr.write(`${c.dim}Expanding query...${c.reset}`);
                    },
                    onExpand: (original, expanded, ms) => {
                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
                        logExpansionTree(original, expanded);
                        process.stderr.write(`${c.dim}Searching ${expanded.length + 1} queries...${c.reset}\n`);
                    },
                    onEmbedStart: (count) => {
                        process.stderr.write(`${c.dim}Embedding ${count} ${count === 1 ? 'query' : 'queries'}...${c.reset}`);
                    },
                    onEmbedDone: (ms) => {
                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
                    },
                    onRerankStart: (chunkCount) => {
                        process.stderr.write(`${c.dim}Reranking ${chunkCount} chunks...${c.reset}`);
                        progress.indeterminate();
                    },
                    onRerankDone: (ms) => {
                        progress.clear();
                        process.stderr.write(`${c.dim} (${formatMs(ms)})${c.reset}\n`);
                    },
                },
            });
        }
        // Post-filter for multi-collection
        if (collectionNames.length > 1) {
            results = results.filter(r => {
                const prefixes = collectionNames.map(n => `qmd://${n}/`);
                return prefixes.some(p => r.file.startsWith(p));
            });
        }
        closeDb();
        if (results.length === 0) {
            printEmptySearchResults(opts.format);
            return;
        }
        // Use first lex/vec query for output context, or original query
        const structuredQueries = parsed?.searches;
        const displayQuery = structuredQueries
            ? (structuredQueries.find(s => s.type === 'lex')?.query || structuredQueries.find(s => s.type === 'vec')?.query || query)
            : query;
        // 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,
            chunkPos: r.bestChunkPos,
            score: r.score,
            context: r.context,
            docid: r.docid,
            explain: r.explain,
        })), displayQuery, { ...opts, limit: results.length });
    }, { maxDuration: 10 * 60 * 1000, name: 'querySearch' });
}
// Parse CLI arguments using util.parseArgs
function parseCLI() {
    const { values, positionals } = parseArgs({
        args: process.argv.slice(2), // Skip node and script path
        options: {
            // Global options
            index: {
                type: "string",
            },
            context: {
                type: "string",
            },
            help: { type: "boolean", short: "h" },
            version: { type: "boolean", short: "v" },
            skill: { type: "boolean" },
            global: { type: "boolean" },
            yes: { type: "boolean" },
            // Search options
            n: { type: "string" },
            "min-score": { type: "string" },
            all: { type: "boolean" },
            full: { type: "boolean" },
            csv: { type: "boolean" },
            md: { type: "boolean" },
            xml: { type: "boolean" },
            files: { type: "boolean" },
            json: { type: "boolean" },
            explain: { type: "boolean" },
            collection: { type: "string", short: "c", multiple: true }, // Filter by collection(s)
            // Collection options
            name: { type: "string" }, // collection name
            mask: { type: "string" }, // glob pattern
            // Embed options
            force: { type: "boolean", short: "f" },
            "max-docs-per-batch": { type: "string" },
            "max-batch-mb": { type: "string" },
            provider: { type: "string" }, // "local" | "openai"
            "embed-endpoint": { type: "string" }, // OpenAI-compatible endpoint URL
            "embed-api-key": { type: "string" }, // Bearer token
            "embed-model-id": { type: "string" }, // Stable model id (default: embeddinggemma)
            "embed-upstream-model": { type: "string" }, // Upstream model name in HTTP body
            "embed-batch-size": { type: "string" }, // Batch size for HTTP provider
            "embed-timeout-ms": { type: "string" }, // Per-request timeout
            "embed-auto-fallback": { type: "boolean" }, // Wrap openai in AutoFallback (local fallback)
            // Update options
            pull: { type: "boolean" }, // git pull before update
            refresh: { type: "boolean" },
            // Get options
            l: { type: "string" }, // max lines
            from: { type: "string" }, // start line
            "max-bytes": { type: "string" }, // max bytes for multi-get
            "line-numbers": { type: "boolean" }, // add line numbers to output
            // Query options
            "candidate-limit": { type: "string", short: "C" },
            "no-rerank": { type: "boolean", default: false },
            intent: { type: "string" },
            // Chunking options
            "chunk-strategy": { type: "string" }, // "regex" (default) or "auto" (AST for code files)
            // MCP HTTP transport options
            http: { type: "boolean" },
            daemon: { type: "boolean" },
            port: { type: "string" },
        },
        allowPositionals: true,
        strict: false, // Allow unknown options to pass through
    });
    // Select index name (default: "index")
    const indexName = values.index;
    if (indexName) {
        setIndexName(indexName);
        setConfigIndexName(indexName);
    }
    // Determine output format
    let format = "cli";
    if (values.csv)
        format = "csv";
    else if (values.md)
        format = "md";
    else if (values.xml)
        format = "xml";
    else if (values.files)
        format = "files";
    else if (values.json)
        format = "json";
    // Default limit: 20 for --files/--json, 5 otherwise
    // --all means return all results (use very large limit)
    const defaultLimit = (format === "files" || format === "json") ? 20 : 5;
    const isAll = !!values.all;
    const opts = {
        format,
        full: !!values.full,
        limit: isAll ? 100000 : (values.n ? parseInt(String(values.n), 10) || defaultLimit : defaultLimit),
        minScore: values["min-score"] ? parseFloat(String(values["min-score"])) || 0 : 0,
        all: isAll,
        collection: values.collection,
        lineNumbers: !!values["line-numbers"],
        candidateLimit: values["candidate-limit"] ? parseInt(String(values["candidate-limit"]), 10) : undefined,
        skipRerank: !!values["no-rerank"],
        explain: !!values.explain,
        intent: values.intent,
        chunkStrategy: parseChunkStrategy(values["chunk-strategy"]),
    };
    return {
        command: positionals[0] || "",
        args: positionals.slice(1),
        query: positionals.slice(1).join(" "),
        opts,
        values,
    };
}
function getSkillInstallDir(globalInstall) {
    return globalInstall
        ? resolve(homedir(), ".agents", "skills", "qmd")
        : resolve(getPwd(), ".agents", "skills", "qmd");
}
function getClaudeSkillLinkPath(globalInstall) {
    return globalInstall
        ? resolve(homedir(), ".claude", "skills", "qmd")
        : resolve(getPwd(), ".claude", "skills", "qmd");
}
function pathExists(path) {
    try {
        lstatSync(path);
        return true;
    }
    catch {
        return false;
    }
}
function removePath(path) {
    const stat = lstatSync(path);
    if (stat.isDirectory() && !stat.isSymbolicLink()) {
        rmSync(path, { recursive: true, force: true });
    }
    else {
        unlinkSync(path);
    }
}
function showSkill() {
    console.log("QMD Skill (embedded)");
    console.log("");
    const content = getEmbeddedQmdSkillContent();
    process.stdout.write(content.endsWith("\n") ? content : content + "\n");
}
function writeEmbeddedSkill(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");
    }
}
function ensureClaudeSymlink(linkPath, targetDir, force) {
    const parentDir = dirname(linkPath);
    if (pathExists(parentDir)) {
        const resolvedTargetDir = realpathSync(dirname(targetDir));
        const resolvedLinkParent = realpathSync(parentDir);
        // If .claude/skills already resolves to the same directory as .agents/skills,
        // the skill is already visible to Claude and creating qmd -> qmd would loop.
        if (resolvedTargetDir === resolvedLinkParent) {
            return false;
        }
    }
    const linkTarget = relativePath(parentDir, targetDir) || ".";
    mkdirSync(parentDir, { recursive: true });
    if (pathExists(linkPath)) {
        const stat = lstatSync(linkPath);
        if (stat.isSymbolicLink() && readlinkSync(linkPath) === linkTarget) {
            return true;
        }
        if (!force) {
            throw new Error(`Claude skill path already exists: ${linkPath} (use --force to replace it)`);
        }
        removePath(linkPath);
    }
    symlinkSync(linkTarget, linkPath, "dir");
    return true;
}
async function shouldCreateClaudeSymlink(linkPath, autoYes) {
    if (autoYes) {
        return true;
    }
    if (!process.stdin.isTTY || !process.stdout.isTTY) {
        console.log(`Tip: create a Claude symlink manually at ${linkPath}`);
        return false;
    }
    const rl = createInterface({
        input: process.stdin,
        output: process.stdout,
    });
    try {
        const answer = await rl.question(`Create a symlink in ${linkPath}? [y/N] `);
        const normalized = answer.trim().toLowerCase();
        return normalized === "y" || normalized === "yes";
    }
    finally {
        rl.close();
    }
}
async function installSkill(globalInstall, force, autoYes) {
    const installDir = getSkillInstallDir(globalInstall);
    writeEmbeddedSkill(installDir, force);
    console.log(`✓ Installed QMD skill to ${installDir}`);
    const claudeLinkPath = getClaudeSkillLinkPath(globalInstall);
    if (!(await shouldCreateClaudeSymlink(claudeLinkPath, autoYes))) {
        return;
    }
    const linked = ensureClaudeSymlink(claudeLinkPath, installDir, force);
    if (linked) {
        console.log(`✓ Linked Claude skill at ${claudeLinkPath}`);
    }
    else {
        console.log(`✓ Claude already sees the skill via ${dirname(claudeLinkPath)}`);
    }
}
function showHelp() {
    console.log("qmd — Quick Markdown Search");
    console.log("");
    console.log("Usage:");
    console.log("  qmd <command> [options]");
    console.log("");
    console.log("Primary commands:");
    console.log("  qmd query <query>             - Hybrid search with auto expansion + reranking (recommended)");
    console.log("  qmd query 'lex:..\\nvec:...'   - Structured query document (you provide lex/vec/hyde lines)");
    console.log("  qmd search <query>            - Full-text BM25 keywords (no LLM)");
    console.log("  qmd vsearch <query>           - Vector similarity only");
    console.log("  qmd get <file>[: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 mcp                       - Start the MCP server (stdio transport for AI agents)");
    console.log("  qmd bench <fixture.json>      - Run search quality benchmarks against a fixture file");
    console.log("");
    console.log("Collections & context:");
    console.log("  qmd collection add/list/remove/rename/show   - Manage indexed folders");
    console.log("  qmd context add/list/rm                      - Attach human-written summaries");
    console.log("  qmd ls [collection[/path]]                   - Inspect indexed files");
    console.log("");
    console.log("Maintenance:");
    console.log("  qmd 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("    --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("    --provider {local,openai}   - Embedding backend (default: local llama.cpp)");
    console.log("    --embed-endpoint <url>      - OpenAI-compatible endpoint (or QMD_EMBED_ENDPOINT)");
    console.log("    --embed-api-key <key>       - Bearer token (or QMD_EMBED_API_KEY)");
    console.log("    --embed-model-id <id>       - Stable model id stored in DB (default: embeddinggemma)");
    console.log("    --embed-upstream-model <m>  - Model name sent in HTTP body (default: same as model-id)");
    console.log("    --embed-batch-size <n>      - Batch size for HTTP provider (default: 64)");
    console.log("    --embed-timeout-ms <n>      - Per-request timeout in ms (default: 30000)");
    console.log("    --embed-auto-fallback       - Wrap openai provider in local fallback (or QMD_EMBED_AUTO_FALLBACK)");
    console.log("  qmd cleanup                   - Clear caches, vacuum DB");
    console.log("");
    console.log("Query syntax (qmd query):");
    console.log("  QMD queries are either a single expand query (no prefix) or a multi-line");
    console.log("  document where every line is typed with lex:, vec:, or hyde:. This grammar");
    console.log("  matches the docs in docs/SYNTAX.md and is enforced in the CLI.");
    console.log("");
    const grammar = [
        `query          = expand_query | query_document ;`,
        `expand_query   = text | explicit_expand ;`,
        `explicit_expand= "expand:" text ;`,
        `query_document = [ intent_line ] { typed_line } ;`,
        `intent_line    = "intent:" text newline ;`,
        `typed_line     = type ":" text newline ;`,
        `type           = "lex" | "vec" | "hyde" ;`,
        `text           = quoted_phrase | plain_text ;`,
        `quoted_phrase  = '"' { character } '"' ;`,
        `plain_text     = { character } ;`,
        `newline        = "\\n" ;`,
    ];
    console.log("  Grammar:");
    for (const line of grammar) {
        console.log(`    ${line}`);
    }
    console.log("");
    console.log("  Examples:");
    console.log("    qmd query \"how does auth work\"                # single-line → implicit expand");
    console.log("    qmd query $'lex: CAP theorem\\nvec: consistency'  # typed query document");
    console.log("    qmd query $'lex: \"exact matches\" sports -baseball'  # phrase + negation lex search");
    console.log("    qmd query $'hyde: Hypothetical answer text'       # hyde-only document");
    console.log("");
    console.log("  Constraints:");
    console.log("    - Standalone expand queries cannot mix with typed lines.");
    console.log("    - Query documents allow only lex:, vec:, or hyde: prefixes.");
    console.log("    - Each typed line must be single-line text with balanced quotes.");
    console.log("");
    console.log("AI agents & integrations:");
    console.log("  - Run `qmd mcp` to expose the MCP server (stdio) to agents/IDEs.");
    console.log("  - `qmd skill install` installs the QMD skill into ./.agents/skills/qmd.");
    console.log("  - Use `qmd skill install --global` for ~/.agents/skills/qmd.");
    console.log("  - `qmd --skill` is kept as an alias for `qmd skill show`.");
    console.log("  - Advanced: `qmd mcp --http ...` and `qmd mcp --http --daemon` are optional for custom transports.");
    console.log("");
    console.log("Global options:");
    console.log("  --index <name>             - Use a named index (default: index)");
    console.log("  QMD_EDITOR_URI             - Editor link template for clickable TTY search output");
    console.log("");
    console.log("Search options:");
    console.log("  -n <num>                   - Max results (default 5, or 20 for --files/--json)");
    console.log("  --all                      - Return all matches (pair with --min-score)");
    console.log("  --min-score <num>          - Minimum similarity score");
    console.log("  --full                     - Output full document instead of snippet");
    console.log("  -C, --candidate-limit <n>  - Max candidates to rerank (default 40, lower = faster)");
    console.log("  --no-rerank                - Skip LLM reranking (use RRF scores only, much faster on CPU)");
    console.log("  --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)");
    console.log("  --json/--csv/--md/--xml/--files - Same formats as search");
    console.log("");
    console.log(`Index: ${getDbPath()}`);
}
async function showVersion() {
    const scriptDir = dirname(fileURLToPath(import.meta.url));
    const pkgPath = resolve(scriptDir, "..", "..", "package.json");
    const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
    let commit = "";
    try {
        commit = execSync(`git -C ${scriptDir} rev-parse --short HEAD`, { encoding: "utf-8", stdio: ["pipe", "pipe", "pipe"] }).trim();
    }
    catch {
        // Not a git repo or git not available
    }
    const versionStr = commit ? `${pkg.version} (${commit})` : pkg.version;
    console.log(`qmd ${versionStr}`);
}
// Main CLI - only run if this is the main module
const __filename = fileURLToPath(import.meta.url);
const argv1 = process.argv[1];
const isMain = argv1 === __filename
    || argv1?.endsWith("/qmd.ts")
    || argv1?.endsWith("/qmd.js")
    || (argv1 != null && realpathSync(argv1) === __filename);
if (isMain) {
    const cli = parseCLI();
    if (cli.values.version) {
        await showVersion();
        process.exit(0);
    }
    if (cli.values.skill) {
        showSkill();
        process.exit(0);
    }
    if (cli.values.help && cli.command === "skill") {
        console.log("Usage: qmd skill <show|install> [options]");
        console.log("");
        console.log("Commands:");
        console.log("  show                 Print the packaged QMD skill");
        console.log("  install              Install into ./.agents/skills/qmd");
        console.log("");
        console.log("Options:");
        console.log("  --global             Install into ~/.agents/skills/qmd");
        console.log("  --yes                Also create the .claude/skills/qmd symlink");
        console.log("  -f, --force          Replace existing install or symlink");
        process.exit(0);
    }
    if (!cli.command || cli.values.help) {
        showHelp();
        process.exit(cli.values.help ? 0 : 1);
    }
    switch (cli.command) {
        case "context": {
            const subcommand = cli.args[0];
            if (!subcommand) {
                console.error("Usage: qmd context <add|list|rm>");
                console.error("");
                console.error("Commands:");
                console.error("  qmd context add [path] \"text\"  - Add context (defaults to current dir)");
                console.error("  qmd context add / \"text\"       - Add global context to all collections");
                console.error("  qmd context list                - List all contexts");
                console.error("  qmd context rm <path>           - Remove context");
                process.exit(1);
            }
            switch (subcommand) {
                case "add": {
                    if (cli.args.length < 2) {
                        console.error("Usage: qmd context add [path] \"text\"");
                        console.error("");
                        console.error("Examples:");
                        console.error("  qmd context add \"Context for current directory\"");
                        console.error("  qmd context add . \"Context for current directory\"");
                        console.error("  qmd context add /subfolder \"Context for subfolder\"");
                        console.error("  qmd context add / \"Global context for all collections\"");
                        console.error("");
                        console.error("  Using virtual paths:");
                        console.error("  qmd context add qmd://journals/ \"Context for entire journals collection\"");
                        console.error("  qmd context add qmd://journals/2024 \"Context for 2024 journals\"");
                        process.exit(1);
                    }
                    let pathArg;
                    let contextText;
                    // Check if first arg looks like a path or if it's the context text
                    const firstArg = cli.args[1] || '';
                    const secondArg = cli.args[2];
                    if (secondArg) {
                        // Two args: path + context
                        pathArg = firstArg;
                        contextText = cli.args.slice(2).join(" ");
                    }
                    else {
                        // One arg: context only (use current directory)
                        pathArg = undefined;
                        contextText = firstArg;
                    }
                    await contextAdd(pathArg, contextText);
                    break;
                }
                case "list": {
                    contextList();
                    break;
                }
                case "rm":
                case "remove": {
                    if (cli.args.length < 2 || !cli.args[1]) {
                        console.error("Usage: qmd context rm <path>");
                        console.error("Examples:");
                        console.error("  qmd context rm /");
                        console.error("  qmd context rm qmd://journals/2024");
                        process.exit(1);
                    }
                    contextRemove(cli.args[1]);
                    break;
                }
                default:
                    console.error(`Unknown subcommand: ${subcommand}`);
                    console.error("Available: add, list, rm");
                    process.exit(1);
            }
            break;
        }
        case "get": {
            if (!cli.args[0]) {
                console.error("Usage: qmd get <filepath>[:line] [--from <line>] [-l <lines>] [--line-numbers]");
                process.exit(1);
            }
            const fromLine = cli.values.from ? parseInt(cli.values.from, 10) : undefined;
            const maxLines = cli.values.l ? parseInt(cli.values.l, 10) : undefined;
            getDocument(cli.args[0], fromLine, maxLines, cli.opts.lineNumbers);
            break;
        }
        case "multi-get": {
            if (!cli.args[0]) {
                console.error("Usage: qmd multi-get <pattern> [-l <lines>] [--max-bytes <bytes>] [--json|--csv|--md|--xml|--files]");
                console.error("  pattern: glob (e.g., 'journals/2025-05*.md') or comma-separated list");
                process.exit(1);
            }
            const maxLinesMulti = cli.values.l ? parseInt(cli.values.l, 10) : undefined;
            const maxBytes = cli.values["max-bytes"] ? parseInt(cli.values["max-bytes"], 10) : DEFAULT_MULTI_GET_MAX_BYTES;
            multiGet(cli.args[0], maxLinesMulti, maxBytes, cli.opts.format);
            break;
        }
        case "ls": {
            listFiles(cli.args[0]);
            break;
        }
        case "collection": {
            const subcommand = cli.args[0];
            switch (subcommand) {
                case "list": {
                    collectionList();
                    break;
                }
                case "add": {
                    const pwd = cli.args[1] || getPwd();
                    const resolvedPwd = pwd === '.' ? getPwd() : getRealPath(resolve(pwd));
                    const globPattern = cli.values.mask || DEFAULT_GLOB;
                    const name = cli.values.name;
                    await collectionAdd(resolvedPwd, globPattern, name);
                    break;
                }
                case "remove":
                case "rm": {
                    if (!cli.args[1]) {
                        console.error("Usage: qmd collection remove <name>");
                        console.error("  Use 'qmd collection list' to see available collections");
                        process.exit(1);
                    }
                    collectionRemove(cli.args[1]);
                    break;
                }
                case "rename":
                case "mv": {
                    if (!cli.args[1] || !cli.args[2]) {
                        console.error("Usage: qmd collection rename <old-name> <new-name>");
                        console.error("  Use 'qmd collection list' to see available collections");
                        process.exit(1);
                    }
                    collectionRename(cli.args[1], cli.args[2]);
                    break;
                }
                case "set-update":
                case "update-cmd": {
                    const name = cli.args[1];
                    const cmd = cli.args.slice(2).join(' ') || null;
                    if (!name) {
                        console.error("Usage: qmd collection update-cmd <name> [command]");
                        console.error("  Set the command to run before indexing (e.g., 'git pull')");
                        console.error("  Omit command to clear it");
                        process.exit(1);
                    }
                    const { updateCollectionSettings, getCollection } = await import("../collections.js");
                    const col = getCollection(name);
                    if (!col) {
                        console.error(`Collection not found: ${name}`);
                        process.exit(1);
                    }
                    updateCollectionSettings(name, { update: cmd });
                    if (cmd) {
                        console.log(`✓ Set update command for '${name}': ${cmd}`);
                    }
                    else {
                        console.log(`✓ Cleared update command for '${name}'`);
                    }
                    break;
                }
                case "include":
                case "exclude": {
                    const name = cli.args[1];
                    if (!name) {
                        console.error(`Usage: qmd collection ${subcommand} <name>`);
                        console.error(`  ${subcommand === 'include' ? 'Include' : 'Exclude'} collection in default queries`);
                        process.exit(1);
                    }
                    const { updateCollectionSettings, getCollection } = await import("../collections.js");
                    const col = getCollection(name);
                    if (!col) {
                        console.error(`Collection not found: ${name}`);
                        process.exit(1);
                    }
                    const include = subcommand === 'include';
                    updateCollectionSettings(name, { includeByDefault: include });
                    console.log(`✓ Collection '${name}' ${include ? 'included in' : 'excluded from'} default queries`);
                    break;
                }
                case "show":
                case "info": {
                    const name = cli.args[1];
                    if (!name) {
                        console.error("Usage: qmd collection show <name>");
                        process.exit(1);
                    }
                    const { getCollection } = await import("../collections.js");
                    const col = getCollection(name);
                    if (!col) {
                        console.error(`Collection not found: ${name}`);
                        process.exit(1);
                    }
                    console.log(`Collection: ${name}`);
                    console.log(`  Path:     ${col.path}`);
                    console.log(`  Pattern:  ${col.pattern}`);
                    console.log(`  Include:  ${col.includeByDefault !== false ? 'yes (default)' : 'no'}`);
                    if (col.update) {
                        console.log(`  Update:   ${col.update}`);
                    }
                    if (col.context) {
                        const ctxCount = Object.keys(col.context).length;
                        console.log(`  Contexts: ${ctxCount}`);
                    }
                    break;
                }
                case "help":
                case undefined: {
                    console.log("Usage: qmd collection <command> [options]");
                    console.log("");
                    console.log("Commands:");
                    console.log("  list                      List all collections");
                    console.log("  add <path> [--name NAME]  Add a collection");
                    console.log("  remove <name>             Remove a collection");
                    console.log("  rename <old> <new>        Rename a collection");
                    console.log("  show <name>               Show collection details");
                    console.log("  update-cmd <name> [cmd]   Set pre-update command (e.g., 'git pull')");
                    console.log("  include <name>            Include in default queries");
                    console.log("  exclude <name>            Exclude from default queries");
                    console.log("");
                    console.log("Examples:");
                    console.log("  qmd collection add ~/notes --name notes");
                    console.log("  qmd collection update-cmd brain 'git pull'");
                    console.log("  qmd collection exclude archive");
                    process.exit(0);
                }
                default:
                    console.error(`Unknown subcommand: ${subcommand}`);
                    console.error("Run 'qmd collection help' for usage");
                    process.exit(1);
            }
            break;
        }
        case "status":
            await showStatus();
            break;
        case "update":
            await updateCollections();
            break;
        case "embed":
            try {
                const maxDocsPerBatch = parseEmbedBatchOption("maxDocsPerBatch", cli.values["max-docs-per-batch"]);
                const maxBatchMb = parseEmbedBatchOption("maxBatchBytes", cli.values["max-batch-mb"]);
                const embedChunkStrategy = parseChunkStrategy(cli.values["chunk-strategy"]);
                // Build embedding provider from CLI flags + env + config file.
                // Backward compat: with no flags / env vars, the factory returns
                // a LocalLlamaCppProvider that delegates to the default LlamaCpp
                // singleton — identical to pre-patch behavior.
                const providerCliKind = parseProviderKind(cli.values["provider"]);
                const providerOpts = buildProviderOpts(cli.values, providerCliKind);
                const embedProvider = createEmbeddingProvider(providerOpts);
                await vectorIndex(DEFAULT_EMBED_MODEL_URI, !!cli.values.force, {
                    maxDocsPerBatch,
                    maxBatchBytes: maxBatchMb === undefined ? undefined : maxBatchMb * 1024 * 1024,
                    chunkStrategy: embedChunkStrategy,
                    embedProvider,
                    providerKind: embedProvider.kind,
                });
            }
            catch (error) {
                if (error instanceof ModelMismatchError) {
                    // Friendlier output for the migration-safety guard
                    console.error(`${c.red}Model mismatch:${c.reset} ${error.message}`);
                }
                else {
                    console.error(error instanceof Error ? error.message : String(error));
                }
                process.exit(1);
            }
            break;
        case "pull": {
            const refresh = cli.values.refresh === undefined ? false : Boolean(cli.values.refresh);
            const models = [
                DEFAULT_EMBED_MODEL_URI,
                DEFAULT_GENERATE_MODEL_URI,
                DEFAULT_RERANK_MODEL_URI,
            ];
            console.log(`${c.bold}Pulling models${c.reset}`);
            const results = await pullModels(models, {
                refresh,
                cacheDir: DEFAULT_MODEL_CACHE_DIR,
            });
            for (const result of results) {
                const size = formatBytes(result.sizeBytes);
                const note = result.refreshed ? "refreshed" : "cached/checked";
                console.log(`- ${result.model} -> ${result.path} (${size}, ${note})`);
            }
            break;
        }
        case "search":
            if (!cli.query) {
                console.error("Usage: qmd search [options] <query>");
                process.exit(1);
            }
            search(cli.query, cli.opts);
            break;
        case "vsearch":
        case "vector-search": // undocumented alias
            if (!cli.query) {
                console.error("Usage: qmd vsearch [options] <query>");
                process.exit(1);
            }
            // Default min-score for vector search is 0.3
            if (!cli.values["min-score"]) {
                cli.opts.minScore = 0.3;
            }
            await vectorSearch(cli.query, cli.opts);
            break;
        case "query":
        case "deep-search": // undocumented alias
            if (!cli.query) {
                console.error("Usage: qmd query [options] <query>");
                process.exit(1);
            }
            await 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.opts.json,
                collection: Array.isArray(benchCollection) ? benchCollection[0] : benchCollection,
            });
            break;
        }
        case "mcp": {
            const sub = cli.args[0]; // stop | status | undefined
            // Cache dir for PID/log files — same dir as the index
            const cacheDir = process.env.XDG_CACHE_HOME
                ? resolve(process.env.XDG_CACHE_HOME, "qmd")
                : resolve(homedir(), ".cache", "qmd");
            const pidPath = resolve(cacheDir, "mcp.pid");
            // Subcommands take priority over flags
            if (sub === "stop") {
                if (!existsSync(pidPath)) {
                    console.log("Not running (no PID file).");
                    process.exit(0);
                }
                const pid = parseInt(readFileSync(pidPath, "utf-8").trim());
                try {
                    process.kill(pid, 0); // alive?
                    process.kill(pid, "SIGTERM");
                    unlinkSync(pidPath);
                    console.log(`Stopped QMD MCP server (PID ${pid}).`);
                }
                catch {
                    unlinkSync(pidPath);
                    console.log("Cleaned up stale PID file (server was not running).");
                }
                process.exit(0);
            }
            if (cli.values.http) {
                const port = Number(cli.values.port) || 8181;
                if (cli.values.daemon) {
                    // Guard: check if already running
                    if (existsSync(pidPath)) {
                        const existingPid = parseInt(readFileSync(pidPath, "utf-8").trim());
                        try {
                            process.kill(existingPid, 0); // alive?
                            console.error(`Already running (PID ${existingPid}). Run 'qmd mcp stop' first.`);
                            process.exit(1);
                        }
                        catch {
                            // Stale PID file — continue
                        }
                    }
                    mkdirSync(cacheDir, { recursive: true });
                    const logPath = resolve(cacheDir, "mcp.log");
                    const logFd = openSync(logPath, "w"); // truncate — fresh log per daemon run
                    const selfPath = fileURLToPath(import.meta.url);
                    const spawnArgs = selfPath.endsWith(".ts")
                        ? ["--import", pathJoin(dirname(selfPath), "..", "..", "node_modules", "tsx", "dist", "esm", "index.mjs"), selfPath, "mcp", "--http", "--port", String(port)]
                        : [selfPath, "mcp", "--http", "--port", String(port)];
                    const child = nodeSpawn(process.execPath, spawnArgs, {
                        stdio: ["ignore", logFd, logFd],
                        detached: true,
                    });
                    child.unref();
                    closeSync(logFd); // parent's copy; child inherited the fd
                    writeFileSync(pidPath, String(child.pid));
                    console.log(`Started on http://localhost:${port}/mcp (PID ${child.pid})`);
                    console.log(`Logs: ${logPath}`);
                    process.exit(0);
                }
                // Foreground HTTP mode — remove top-level cursor handlers so the
                // async cleanup handlers in startMcpHttpServer actually run.
                process.removeAllListeners("SIGTERM");
                process.removeAllListeners("SIGINT");
                const { startMcpHttpServer } = await import("../mcp/server.js");
                try {
                    await startMcpHttpServer(port);
                }
                catch (e) {
                    if (e?.code === "EADDRINUSE") {
                        console.error(`Port ${port} already in use. Try a different port with --port.`);
                        process.exit(1);
                    }
                    throw e;
                }
            }
            else {
                // Default: stdio transport
                const { startMcpServer } = await import("../mcp/server.js");
                await startMcpServer();
            }
            break;
        }
        case "skill": {
            const subcommand = cli.args[0];
            switch (subcommand) {
                case "show": {
                    showSkill();
                    break;
                }
                case "install": {
                    try {
                        await installSkill(Boolean(cli.values.global), Boolean(cli.values.force), Boolean(cli.values.yes));
                    }
                    catch (error) {
                        console.error(error instanceof Error ? error.message : String(error));
                        process.exit(1);
                    }
                    break;
                }
                case "help":
                case undefined: {
                    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("");
                    console.log("Options:");
                    console.log("  --global             Install into ~/.agents/skills/qmd");
                    console.log("  --yes                Also create the .claude/skills/qmd symlink");
                    console.log("  -f, --force          Replace existing install or symlink");
                    process.exit(0);
                }
                default:
                    console.error(`Unknown subcommand: ${subcommand}`);
                    console.error("Run 'qmd skill help' for usage");
                    process.exit(1);
            }
            break;
        }
        case "cleanup": {
            const db = getDb();
            // 1. Clear llm_cache
            const cacheCount = deleteLLMCache(db);
            console.log(`${c.green}✓${c.reset} Cleared ${cacheCount} cached API responses`);
            // 2. Remove orphaned vectors
            const orphanedVecs = cleanupOrphanedVectors(db);
            if (orphanedVecs > 0) {
                console.log(`${c.green}✓${c.reset} Removed ${orphanedVecs} orphaned embedding chunks`);
            }
            else {
                console.log(`${c.dim}No orphaned embeddings to remove${c.reset}`);
            }
            // 3. Remove inactive documents
            const inactiveDocs = deleteInactiveDocuments(db);
            if (inactiveDocs > 0) {
                console.log(`${c.green}✓${c.reset} Removed ${inactiveDocs} inactive document records`);
            }
            // 4. Vacuum to reclaim space
            vacuumDatabase(db);
            console.log(`${c.green}✓${c.reset} Database vacuumed`);
            closeDb();
            break;
        }
        default:
            console.error(`Unknown command: ${cli.command}`);
            console.error("Run 'qmd --help' for usage.");
            process.exit(1);
    }
    if (cli.command !== "mcp") {
        await disposeDefaultLlamaCpp();
        process.exit(0);
    }
} // end if (main module)