qmd/src/qmd.ts

#!/usr/bin/env bun
import { Database } from "bun:sqlite";
import { Glob, $ } from "bun";
import { parseArgs } from "util";
import * as sqliteVec from "sqlite-vec";
import {
  getDb,
  closeDb,
  getDbPath,
  getPwd,
  getRealPath,
  homedir,
  resolve,
  setCustomIndexName,
  searchFTS,
  searchVec,
  reciprocalRankFusion,
  extractSnippet,
  getContextForFile,
  getContextForPath,
  listCollections,
  removeCollection,
  renameCollection,
  findSimilarFiles,
  matchFilesByGlob,
  getHashesNeedingEmbedding,
  getHashesForEmbedding,
  clearAllEmbeddings,
  insertEmbedding,
  getDocument as storeGetDocument,
  getMultipleDocuments as storeMultiGetDocuments,
  getStatus,
  hashContent,
  extractTitle,
  formatDocForEmbedding,
  formatQueryForEmbedding,
  chunkDocument,
  ensureVecTable,
  clearCache,
  getCacheKey,
  getCachedResult,
  setCachedResult,
  getIndexHealth,
  parseVirtualPath,
  buildVirtualPath,
  isVirtualPath,
  resolveVirtualPath,
  toVirtualPath,
  insertContent,
  insertDocument,
  findActiveDocument,
  updateDocumentTitle,
  updateDocument,
  deactivateDocument,
  getActiveDocumentPaths,
  cleanupOrphanedContent,
  deleteOllamaCache,
  deleteInactiveDocuments,
  cleanupOrphanedVectors,
  cleanupDuplicateCollections,
  vacuumDatabase,
  getCollectionsWithoutContext,
  getTopLevelPathsWithoutContext,
  handelize,
  OLLAMA_URL,
  DEFAULT_EMBED_MODEL,
  DEFAULT_QUERY_MODEL,
  DEFAULT_RERANK_MODEL,
  DEFAULT_GLOB,
  DEFAULT_MULTI_GET_MAX_BYTES,
} from "./store.js";
import type { SearchResult, RankedResult } from "./store.js";
import {
  formatSearchResults,
  formatDocuments,
  escapeXml,
  escapeCSV,
  type OutputFormat,
} from "./formatter.js";
import {
  getCollection as getCollectionFromYaml,
  listCollections as yamlListCollections,
  addContext as yamlAddContext,
  removeContext as yamlRemoveContext,
  setGlobalContext,
  listAllContexts,
} from "./collections.js";

// Chunking: ~2000 tokens per chunk, ~3 bytes/token = 6KB
const CHUNK_BYTE_SIZE = 6 * 1024;

// Terminal colors (respects NO_COLOR env)
const useColor = !process.env.NO_COLOR && process.stdout.isTTY;
const c = {
  reset: useColor ? "\x1b[0m" : "",
  dim: useColor ? "\x1b[2m" : "",
  bold: useColor ? "\x1b[1m" : "",
  cyan: useColor ? "\x1b[36m" : "",
  yellow: useColor ? "\x1b[33m" : "",
  green: useColor ? "\x1b[32m" : "",
  magenta: useColor ? "\x1b[35m" : "",
  blue: useColor ? "\x1b[34m" : "",
};

// Terminal cursor control
const cursor = {
  hide() { process.stderr.write('\x1b[?25l'); },
  show() { process.stderr.write('\x1b[?25h'); },
};

// 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
const progress = {
  set(percent: number) {
    process.stderr.write(`\x1b]9;4;1;${Math.round(percent)}\x07`);
  },
  clear() {
    process.stderr.write(`\x1b]9;4;0\x07`);
  },
  indeterminate() {
    process.stderr.write(`\x1b]9;4;3\x07`);
  },
  error() {
    process.stderr.write(`\x1b]9;4;2\x07`);
  },
};

// Format seconds into human-readable ETA
function formatETA(seconds: number): string {
  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: Database): void {
  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: string,
  collectionPath: string,
  existingPaths: Set<string>
): string {
  // Get path relative to collection (include collection dir name)
  const collectionDir = collectionPath.replace(/\/$/, '');
  const collectionName = collectionDir.split('/').pop() || '';

  let relativePath: string;
  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;
}

// Auto-pull model if not found
async function ensureModelAvailable(model: string): Promise<void> {
  try {
    const response = await fetch(`${OLLAMA_URL}/api/show`, {
      method: "POST",
      headers: { "Content-Type": "application/json" },
      body: JSON.stringify({ name: model }),
    });
    if (response.ok) return;
  } catch {
    // Continue to pull attempt
  }

  console.log(`Model ${model} not found. Pulling...`);
  progress.indeterminate();

  const pullResponse = await fetch(`${OLLAMA_URL}/api/pull`, {
    method: "POST",
    headers: { "Content-Type": "application/json" },
    body: JSON.stringify({ name: model, stream: false }),
  });

  if (!pullResponse.ok) {
    progress.error();
    throw new Error(`Failed to pull model ${model}: ${pullResponse.status} - ${await pullResponse.text()}`);
  }

  progress.clear();
  console.log(`Model ${model} pulled successfully.`);
}

async function getEmbedding(text: string, model: string, isQuery: boolean = false, title?: string, retried: boolean = false): Promise<number[]> {
  const input = isQuery ? formatQueryForEmbedding(text) : formatDocForEmbedding(text, title);

  const response = await fetch(`${OLLAMA_URL}/api/embed`, {
    method: "POST",
    headers: { "Content-Type": "application/json" },
    body: JSON.stringify({ model, input }),
  });
  if (!response.ok) {
    const errorText = await response.text();
    if (!retried && (errorText.includes("not found") || errorText.includes("does not exist"))) {
      await ensureModelAvailable(model);
      return getEmbedding(text, model, isQuery, title, true);
    }
    throw new Error(`Ollama API error: ${response.status} - ${errorText}`);
  }
  const data = await response.json() as { embeddings: number[][] };
  return data.embeddings[0];
}

// Qwen3-Reranker prompt format (trained for yes/no relevance classification)
const RERANK_SYSTEM = `Judge whether the Document meets the requirements based on the Query and the Instruct provided. Note that the answer can only be "yes" or "no".`;

function formatRerankPrompt(query: string, title: string, doc: string): string {
  return `<Instruct>: Determine if this document from a Shopify knowledge base is relevant to the search query. The query may reference specific Shopify programs, competitions, features, or named concepts (e.g., "Build a Business" competition, "Shop Pay", "Polaris"). Match documents that discuss the queried topic, even if phrasing differs.
<Query>: ${query}
<Document Title>: ${title}
<Document>: ${doc}`;
}

type LogProb = { token: string; logprob: number };
type RerankResponse = {
  response: string;
  logprobs?: LogProb[];
};

function parseRerankResponse(data: RerankResponse): number {
  if (!data.logprobs || data.logprobs.length === 0) {
    throw new Error("Reranker response missing logprobs");
  }

  const firstToken = data.logprobs[0];
  const token = firstToken.token.toLowerCase().trim();
  const confidence = Math.exp(firstToken.logprob);

  if (token === "yes") {
    return confidence;
  }
  if (token === "no") {
    return (1 - confidence) * 0.3;
  }

  throw new Error(`Unexpected reranker token: "${token}"`);
}

async function rerankSingle(prompt: string, model: string, db?: Database, retried: boolean = false): Promise<number> {
  // Use generate with raw template for qwen3-reranker format
  // Include empty <think> tags as per HuggingFace reference implementation
  const fullPrompt = `<|im_start|>system
${RERANK_SYSTEM}<|im_end|>
<|im_start|>user
${prompt}<|im_end|>
<|im_start|>assistant
<think>

</think>

`;

  const requestBody = {
    model,
    prompt: fullPrompt,
    raw: true,
    stream: false,
    logprobs: true,
    options: { num_predict: 1 },
  };

  // Check cache
  const cacheKey = db ? getCacheKey(`${OLLAMA_URL}/api/generate`, requestBody) : "";
  if (db) {
    const cached = getCachedResult(db, cacheKey);
    if (cached) {
      const data = JSON.parse(cached) as RerankResponse;
      return parseRerankResponse(data);
    }
  }

  const response = await fetch(`${OLLAMA_URL}/api/generate`, {
    method: "POST",
    headers: { "Content-Type": "application/json" },
    body: JSON.stringify(requestBody),
  });

  if (!response.ok) {
    const errorText = await response.text();
    if (!retried && (errorText.includes("not found") || errorText.includes("does not exist"))) {
      await ensureModelAvailable(model);
      return rerankSingle(prompt, model, db, true);
    }
    throw new Error(`Ollama API error: ${response.status} - ${errorText}`);
  }

  const data = await response.json() as RerankResponse;

  // Cache the result
  if (db) {
    setCachedResult(db, cacheKey, JSON.stringify(data));
  }

  return parseRerankResponse(data);
}

async function rerank(query: string, documents: { file: string; text: string }[], model: string = DEFAULT_RERANK_MODEL, db?: Database): Promise<{ file: string; score: number }[]> {
  const results: { file: string; score: number }[] = [];
  const total = documents.length;
  const PARALLEL = 5;

  process.stderr.write(`Reranking ${total} documents with ${model} (parallel: ${PARALLEL})...\n`);
  progress.indeterminate();

  // Process in parallel batches
  for (let i = 0; i < documents.length; i += PARALLEL) {
    const batch = documents.slice(i, i + PARALLEL);
    const batchResults = await Promise.all(
      batch.map(async (doc) => {
        try {
          // Extract title from filename for reranker context
          const title = doc.file.split('/').pop()?.replace(/\.md$/, '') || doc.file;
          const prompt = formatRerankPrompt(query, title, doc.text.slice(0, 4000));
          const score = await rerankSingle(prompt, model, db);
          return { file: doc.file, score };
        } catch (err) {
          return { file: doc.file, score: 0 };
        }
      })
    );
    results.push(...batchResults);

    const processed = Math.min(i + PARALLEL, total);
    progress.set((processed / total) * 100);
    process.stderr.write(`\rReranking: ${processed}/${total}`);
  }

  progress.clear();
  process.stderr.write("\n");

  return results.sort((a, b) => b.score - a.score);
}

function formatTimeAgo(date: Date): string {
  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 formatBytes(bytes: number): string {
  if (bytes < 1024) return `${bytes} B`;
  if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(1)} KB`;
  if (bytes < 1024 * 1024 * 1024) return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
  return `${(bytes / (1024 * 1024 * 1024)).toFixed(1)} GB`;
}

function showStatus(): void {
  const dbPath = getDbPath();
  const db = getDb();

  // Cleanup any duplicate collections
  cleanupDuplicateCollections(db);

  // Index size
  let indexSize = 0;
  try {
    const stat = Bun.file(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() as { count: number };
  const vectorCount = db.prepare(`SELECT COUNT(*) as count FROM content_vectors`).get() as { count: number };
  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() as { latest: string | null };

  console.log(`${c.bold}QMD Status${c.reset}\n`);
  console.log(`Index: ${dbPath}`);
  console.log(`Size:  ${formatBytes(indexSize)}\n`);

  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<string, { path_prefix: string; context: string }[]>();

  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
    });
  }

  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(`    ${c.dim}Path:${c.reset}     ${col.pwd}`);
      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) {
      console.log(`  qmd ls ${collections[0].name}`);
    }
    console.log(`  ${c.dim}# Get a document${c.reset}`);
    if (collections.length > 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) {
      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}`);
  }

  closeDb();
}

async function updateCollections(): Promise<void> {
  const db = getDb();
  cleanupDuplicateCollections(db);

  // 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;
  }

  // Don't close db here - indexFiles will reuse it and close at the end
  console.log(`${c.bold}Updating ${collections.length} collection(s)...${c.reset}\n`);

  for (let i = 0; i < collections.length; i++) {
    const col = collections[i];
    console.log(`${c.cyan}[${i + 1}/${collections.length}]${c.reset} ${c.bold}${col.name}${c.reset}`);
    console.log(`${c.dim}    Path: ${col.pwd}${c.reset}`);
    console.log(`${c.dim}    Pattern: ${col.glob_pattern}${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 = Bun.spawn(["/usr/bin/env", "bash", "-c", yamlCol.update], {
          cwd: col.pwd,
          stdout: "pipe",
          stderr: "pipe",
        });

        const output = await new Response(proc.stdout).text();
        const errorOutput = await new Response(proc.stderr).text();
        const exitCode = await proc.exited;

        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);
      }
    }

    await indexFiles(col.pwd, col.glob_pattern, col.name);
    console.log("");
  }

  console.log(`${c.green}✓ All collections updated.${c.reset}`);
}

/**
 * Detect which collection (if any) contains the given filesystem path.
 * Returns { collectionId, collectionName, relativePath } or null if not in any collection.
 */
function detectCollectionFromPath(db: Database, fsPath: string): { collectionName: string; relativePath: string } | null {
  const realPath = getRealPath(fsPath);

  // Find collections that this path is under from YAML
  const allCollections = yamlListCollections();

  // Find longest matching path
  let bestMatch: { name: string; path: string } | null = 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: string | undefined, contextText: string): Promise<void> {
  const db = getDb();

  // Handle "/" as global context (applies to all collections)
  if (pathArg === '/') {
    setGlobalContext(contextText);
    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);

    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);

  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(): void {
  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: string): void {
  if (pathArg === '/') {
    // Remove global context
    setGlobalContext(undefined);
    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 contextCheck(): void {
  const db = getDb();

  // Get collections without any context
  const collectionsWithoutContext = getCollectionsWithoutContext(db);

  // Get all collections to check for missing path contexts
  const allCollections = listCollections(db);

  if (collectionsWithoutContext.length === 0 && allCollections.length > 0) {
    // Check if all collections have contexts
    console.log(`\n${c.green}✓${c.reset} ${c.bold}All collections have context configured${c.reset}\n`);
  }

  if (collectionsWithoutContext.length > 0) {
    console.log(`\n${c.yellow}Collections without any context:${c.reset}\n`);

    for (const coll of collectionsWithoutContext) {
      console.log(`${c.cyan}${coll.name}${c.reset}`);
      console.log(`  ${c.dim}Path: ${coll.pwd}${c.reset}`);
      console.log(`  ${c.dim}Documents: ${coll.doc_count}${c.reset}`);
      console.log(`  ${c.dim}Suggestion: qmd context add qmd://${coll.name}/ "Description of ${coll.name}"${c.reset}\n`);
    }
  }

  // Check for top-level paths without context within collections that DO have context
  const collectionsWithContext = allCollections.filter(c =>
    !collectionsWithoutContext.some(cwc => cwc.id === c.id)
  );

  let hasPathSuggestions = false;

  for (const coll of collectionsWithContext) {
    const missingPaths = getTopLevelPathsWithoutContext(db, coll.id);

    if (missingPaths.length > 0) {
      if (!hasPathSuggestions) {
        console.log(`${c.yellow}Top-level directories without context:${c.reset}\n`);
        hasPathSuggestions = true;
      }

      console.log(`${c.cyan}${coll.name}${c.reset}`);
      for (const path of missingPaths) {
        console.log(`  ${path}`);
        console.log(`    ${c.dim}Suggestion: qmd context add qmd://${coll.name}/${path} "Description of ${path}"${c.reset}`);
      }
      console.log('');
    }
  }

  if (collectionsWithoutContext.length === 0 && !hasPathSuggestions) {
    console.log(`${c.dim}All collections and major paths have context configured.${c.reset}`);
    console.log(`${c.dim}Use 'qmd context list' to see all configured contexts.${c.reset}\n`);
  }

  closeDb();
}

function getDocument(filename: string, fromLine?: number, maxLines?: number): void {
  const db = getDb();

  // Parse :linenum suffix from filename (e.g., "file.md:100")
  let inputPath = filename;
  const colonMatch = inputPath.match(/:(\d+)$/);
  if (colonMatch && !fromLine) {
    fromLine = parseInt(colonMatch[1], 10);
    inputPath = inputPath.slice(0, -colonMatch[0].length);
  }

  let doc: { collectionName: string; path: string; body: string } | null = null;
  let virtualPath: string;

  // 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) as typeof doc;

    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}`) as typeof doc;
    }

    virtualPath = inputPath;
  } else {
    // Handle filesystem paths
    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) as typeof doc;
    }

    // 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}`) as typeof doc;
    }

    if (doc) {
      virtualPath = buildVirtualPath(doc.collectionName, doc.path);
    } else {
      virtualPath = inputPath;
    }
  }

  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;

  // Apply line filtering if specified
  if (fromLine !== undefined || maxLines !== undefined) {
    const lines = output.split('\n');
    const start = (fromLine || 1) - 1; // Convert to 0-indexed
    const end = maxLines !== undefined ? start + maxLines : lines.length;
    output = lines.slice(start, end).join('\n');
  }

  // 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: string, maxLines?: number, maxBytes: number = DEFAULT_MULTI_GET_MAX_BYTES, format: OutputFormat = "cli"): void {
  const db = getDb();

  // Check if it's a comma-separated list or a glob pattern
  const isCommaSeparated = pattern.includes(',') && !pattern.includes('*') && !pattern.includes('?');

  let files: { filepath: string; displayPath: string; bodyLength: number; collection?: string; path?: string }[];

  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: { virtual_path: string; body_length: number; collection: string; path: string } | null = 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) as typeof doc;
        }
      } 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) as typeof doc;

        // 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}`) as typeof doc;
        }
      }

      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: { file: string; displayPath: string; title: string; body: string; context: string | null; skipped: boolean; skipReason?: string }[] = [];

  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) as { body: string; title: string } | null;

    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: string | null): string => {
      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?: string): void {
  const db = getDb();

  if (!pathArg) {
    // No argument - list all collections
    const yamlCollections = yamlListCollections();

    if (yamlCollections.length === 0) {
      console.log("No collections found. Run 'qmd 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) as { file_count: number } | null;

      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: string;
  let pathPrefix: string | null = 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: string;
  let params: any[];

  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) as { path: string; title: string; modified_at: string; size: number }[];

  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: Date): string {
  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(): void {
  const db = getDb();
  const collections = listCollections(db);

  if (collections.length === 0) {
    console.log("No collections found. Run 'qmd add .' to create one.");
    closeDb();
    return;
  }

  console.log(`${c.bold}Collections (${collections.length}):${c.reset}\n`);

  for (const coll of collections) {
    const updatedAt = new Date(coll.updated_at);
    const timeAgo = formatTimeAgo(updatedAt);

    console.log(`${c.cyan}${coll.name}${c.reset}`);
    console.log(`  ${c.dim}Path:${c.reset}     ${coll.pwd}`);
    console.log(`  ${c.dim}Pattern:${c.reset}  ${coll.glob_pattern}`);
    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: string, globPattern: string, name?: string): Promise<void> {
  // If name not provided, generate from pwd basename
  if (!name) {
    const parts = pwd.split('/').filter(Boolean);
    name = parts[parts.length - 1] || 'root';
  }

  // Check if collection with this name already exists in YAML
  const existing = getCollectionFromYaml(name);
  if (existing) {
    console.error(`${c.yellow}Collection '${name}' 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}`);
    console.error(`  Path: ${pwd}`);
    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
  const { addCollection } = await import("./collections.js");
  addCollection(name, pwd, globPattern);

  // Create the collection and index files
  console.log(`Creating collection '${name}'...`);
  await indexFiles(pwd, globPattern, name);
  console.log(`${c.green}✓${c.reset} Collection '${name}' created successfully`);
}

function collectionRemove(name: string): void {
  // 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);
  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: string, newName: string): void {
  // 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);
  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?: string, globPattern: string = DEFAULT_GLOB, collectionName?: string): Promise<void> {
  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 glob = new Glob(globPattern);
  const files: string[] = [];
  for await (const file of glob.scan({ cwd: resolvedPwd, onlyFiles: true, followSymlinks: true })) {
    // Skip node_modules, hidden folders (.*), and other common excludes
    const parts = file.split("/");
    const shouldSkip = parts.some(part =>
      part === "node_modules" ||
      part.startsWith(".") ||
      excludeDirs.includes(part)
    );
    if (!shouldSkip) {
      files.push(file);
    }
  }

  const total = files.length;
  if (total === 0) {
    progress.clear();
    console.log("No files found matching pattern.");
    closeDb();
    return;
  }

  let indexed = 0, updated = 0, unchanged = 0, processed = 0;
  const seenPaths = new Set<string>();
  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);

    const content = await Bun.file(filepath).text();
    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 = await Bun.file(filepath).stat();
        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 = await Bun.file(filepath).stat();
      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)}` : "";
    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) {
    console.log(`\nRun 'qmd embed' to update embeddings (${needsEmbedding} unique hashes need vectors)`);
  }

  closeDb();
}

function renderProgressBar(percent: number, width: number = 30): string {
  const filled = Math.round((percent / 100) * width);
  const empty = width - filled;
  const bar = "█".repeat(filled) + "░".repeat(empty);
  return bar;
}

async function vectorIndex(model: string = DEFAULT_EMBED_MODEL, force: boolean = false): Promise<void> {
  const db = getDb();
  const now = new Date().toISOString();

  // If force, clear all vectors
  if (force) {
    console.log(`${c.yellow}Force re-indexing: clearing all vectors...${c.reset}`);
    clearAllEmbeddings(db);
  }

  // Find unique hashes that need embedding (from active documents)
  const hashesToEmbed = getHashesForEmbedding(db);

  if (hashesToEmbed.length === 0) {
    console.log(`${c.green}✓ All content hashes already have embeddings.${c.reset}`);
    closeDb();
    return;
  }

  // Prepare documents with chunks
  type ChunkItem = { hash: string; title: string; text: string; seq: number; pos: number; bytes: number; displayName: string };
  const allChunks: ChunkItem[] = [];
  let multiChunkDocs = 0;

  for (const item of hashesToEmbed) {
    const encoder = new TextEncoder();
    const bodyBytes = encoder.encode(item.body).length;
    if (bodyBytes === 0) continue; // Skip empty

    const title = extractTitle(item.body, item.path);
    const displayName = item.path;
    const chunks = chunkDocument(item.body, CHUNK_BYTE_SIZE);

    if (chunks.length > 1) multiChunkDocs++;

    for (let seq = 0; seq < chunks.length; seq++) {
      allChunks.push({
        hash: item.hash,
        title,
        text: chunks[seq].text,
        seq,
        pos: chunks[seq].pos,
        bytes: encoder.encode(chunks[seq].text).length,
        displayName,
      });
    }
  }

  if (allChunks.length === 0) {
    console.log(`${c.green}✓ No non-empty documents to embed.${c.reset}`);
    closeDb();
    return;
  }

  const totalBytes = allChunks.reduce((sum, c) => sum + c.bytes, 0);
  const totalChunks = allChunks.length;
  const totalDocs = hashesToEmbed.length;

  console.log(`${c.bold}Embedding ${totalDocs} documents${c.reset} ${c.dim}(${totalChunks} chunks, ${formatBytes(totalBytes)})${c.reset}`);
  if (multiChunkDocs > 0) {
    console.log(`${c.dim}${multiChunkDocs} documents split into multiple chunks${c.reset}`);
  }
  console.log(`${c.dim}Model: ${model}${c.reset}\n`);

  // Hide cursor during embedding
  cursor.hide();

  // Get embedding dimensions from first chunk
  progress.indeterminate();
  const firstEmbedding = await getEmbedding(allChunks[0].text, model, false, allChunks[0].title);
  ensureVecTable(db, firstEmbedding.length);

  let chunksEmbedded = 0, errors = 0, bytesProcessed = 0;
  const startTime = Date.now();

  // Insert first chunk
  insertEmbedding(db, allChunks[0].hash, allChunks[0].seq, allChunks[0].pos, new Float32Array(firstEmbedding), model, now);
  chunksEmbedded++;
  bytesProcessed += allChunks[0].bytes;

  for (let i = 1; i < allChunks.length; i++) {
    const chunk = allChunks[i];
    try {
      const embedding = await getEmbedding(chunk.text, model, false, chunk.title);
      insertEmbedding(db, chunk.hash, chunk.seq, chunk.pos, new Float32Array(embedding), model, now);
      chunksEmbedded++;
      bytesProcessed += chunk.bytes;
    } catch (err) {
      errors++;
      bytesProcessed += chunk.bytes;
      progress.error();
      console.error(`\n${c.yellow}⚠ Error embedding "${chunk.displayName}" chunk ${chunk.seq}: ${err}${c.reset}`);
    }

    const percent = (bytesProcessed / totalBytes) * 100;
    progress.set(percent);

    const elapsed = (Date.now() - startTime) / 1000;
    const bytesPerSec = bytesProcessed / elapsed;
    const remainingBytes = totalBytes - 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 = errors > 0 ? ` ${c.yellow}${errors} err${c.reset}` : "";

    process.stderr.write(`\r${c.cyan}${bar}${c.reset} ${c.bold}${percentStr}%${c.reset} ${c.dim}${chunksEmbedded}/${totalChunks}${c.reset}${errStr} ${c.dim}${throughput} ETA ${eta}${c.reset}   `);
  }

  progress.clear();
  cursor.show();
  const totalTimeSec = (Date.now() - startTime) / 1000;
  const avgThroughput = formatBytes(totalBytes / totalTimeSec);

  console.log(`\r${c.green}${renderProgressBar(100)}${c.reset} ${c.bold}100%${c.reset}                                    `);
  console.log(`\n${c.green}✓ Done!${c.reset} Embedded ${c.bold}${chunksEmbedded}${c.reset} chunks from ${c.bold}${totalDocs}${c.reset} documents in ${c.bold}${formatETA(totalTimeSec)}${c.reset} ${c.dim}(${avgThroughput}/s)${c.reset}`);
  if (errors > 0) {
    console.log(`${c.yellow}⚠ ${errors} chunks failed${c.reset}`);
  }
  closeDb();
}

// Sanitize a term for FTS5: remove punctuation except apostrophes
function sanitizeFTS5Term(term: string): string {
  // 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: string): string {
  // 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: number): number {
  // 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));
}

function normalizeScores(results: SearchResult[]): SearchResult[] {
  if (results.length === 0) return results;
  const maxScore = Math.max(...results.map(r => r.score));
  const minScore = Math.min(...results.map(r => r.score));
  const range = maxScore - minScore || 1;
  return results.map(r => ({ ...r, score: (r.score - minScore) / range }));
}

// Reciprocal Rank Fusion: combines multiple ranked lists
// RRF score = sum(1 / (k + rank)) across all lists where doc appears
// k=60 is standard, provides good balance between top and lower ranks
export type RankedResult = { file: string; displayPath: string; title: string; body: string; score: number };

function reciprocalRankFusion(
  resultLists: RankedResult[][],
  weights: number[] = [],  // Weight per result list (default 1.0)
  k: number = 60
): RankedResult[] {
  const scores = new Map<string, { score: number; displayPath: string; title: string; body: string; bestRank: number }>();

  for (let listIdx = 0; listIdx < resultLists.length; listIdx++) {
    const results = resultLists[listIdx];
    const weight = weights[listIdx] ?? 1.0;
    for (let rank = 0; rank < results.length; rank++) {
      const doc = results[rank];
      const rrfScore = weight / (k + rank + 1);
      const existing = scores.get(doc.file);
      if (existing) {
        existing.score += rrfScore;
        existing.bestRank = Math.min(existing.bestRank, rank);
      } else {
        scores.set(doc.file, { score: rrfScore, displayPath: doc.displayPath, title: doc.title, body: doc.body, bestRank: rank });
      }
    }
  }

  // Add bonus for best rank: documents that ranked #1-3 in any list get a boost
  // This prevents dilution of exact matches by expansion queries
  return Array.from(scores.entries())
    .map(([file, { score, displayPath, title, body, bestRank }]) => {
      let bonus = 0;
      if (bestRank === 0) bonus = 0.05;  // Ranked #1 somewhere
      else if (bestRank <= 2) bonus = 0.02;  // Ranked top-3 somewhere
      return { file, displayPath, title, body, score: score + bonus };
    })
    .sort((a, b) => b.score - a.score);
}

type OutputOptions = {
  format: OutputFormat;
  full: boolean;
  limit: number;
  minScore: number;
  all?: boolean;
  collection?: string;  // Filter by collection name (pwd suffix match)
  lineNumbers?: boolean; // Add line numbers to output
};

// Extract snippet with more context lines for CLI display
function extractSnippetWithContext(body: string, query: string, contextLines = 3, chunkPos?: number): { line: number; snippet: string; hasMatch: boolean } {
  // If chunkPos provided, focus search on that area
  let lineOffset = 0;
  let searchBody = body;
  if (chunkPos && chunkPos > 0) {
    const contextStart = Math.max(0, chunkPos - 200);
    searchBody = body.slice(contextStart);
    if (contextStart > 0) {
      lineOffset = body.slice(0, contextStart).split('\n').length - 1;
    }
  }

  const lines = searchBody.split('\n');
  const queryTerms = query.toLowerCase().split(/\s+/).filter(t => t.length > 0);
  let bestLine = 0, bestScore = -1;

  for (let i = 0; i < lines.length; i++) {
    const lineLower = lines[i].toLowerCase();
    let score = 0;
    for (const term of queryTerms) {
      if (lineLower.includes(term)) score++;
    }
    if (score > bestScore) {
      bestScore = score;
      bestLine = i;
    }
  }

  // No query match found - return beginning of chunk area or file
  if (bestScore <= 0) {
    const preview = lines.slice(0, contextLines * 2).join('\n').trim();
    return { line: lineOffset + 1, snippet: preview, hasMatch: false };
  }

  const startLine = Math.max(0, bestLine - contextLines);
  const endLine = Math.min(lines.length, bestLine + contextLines + 1);
  const snippet = lines.slice(startLine, endLine).join('\n').trim();
  return { line: lineOffset + bestLine + 1, snippet, hasMatch: true };
}

// Highlight query terms in text (skip short words < 3 chars)
function highlightTerms(text: string, query: string): string {
  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: number): string {
  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}`;
}

// Shorten directory path for display - relative to $HOME (used for context paths, not documents)
function shortPath(dirpath: string): string {
  const home = homedir();
  if (dirpath.startsWith(home)) {
    return '~' + dirpath.slice(home.length);
  }
  return dirpath;
}

// Add line numbers to text content
function addLineNumbers(text: string, startLine: number = 1): string {
  const lines = text.split('\n');
  return lines.map((line, i) => `${startLine + i}: ${line}`).join('\n');
}

function outputResults(results: { file: string; displayPath: string; title: string; body: string; score: number; context?: string | null; chunkPos?: number; hash?: string; docid?: string }[], query: string, opts: OutputOptions): void {
  const filtered = results.filter(r => r.score >= opts.minScore).slice(0, opts.limit);

  if (filtered.length === 0) {
    console.log("No results found above minimum score threshold.");
    return;
  }

  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).snippet : undefined;
      if (opts.lineNumbers) {
        if (body) body = addLineNumbers(body);
        if (snippet) snippet = addLineNumbers(snippet);
      }
      return {
        ...(docid && { docid: `#${docid}` }),
        score: Math.round(row.score * 100) / 100,
        file: row.displayPath,
        title: row.title,
        ...(row.context && { context: row.context }),
        ...(body && { body }),
        ...(snippet && { snippet }),
      };
    });
    console.log(JSON.stringify(output, null, 2));
  } else if (opts.format === "files") {
    // Simple docid,score,filepath,context output
    for (const row of filtered) {
      const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : "");
      const ctx = row.context ? `,"${row.context.replace(/"/g, '""')}"` : "";
      console.log(`#${docid},${row.score.toFixed(2)},${row.displayPath}${ctx}`);
    }
  } else if (opts.format === "cli") {
    for (let i = 0; i < filtered.length; i++) {
      const row = filtered[i];
      const { line, snippet, hasMatch } = extractSnippetWithContext(row.body, query, 2, row.chunkPos);
      const docid = row.docid || (row.hash ? row.hash.slice(0, 6) : undefined);

      // Line 1: filepath with docid
      const path = row.displayPath;
      const lineInfo = hasMatch ? `:${line}` : "";
      const docidStr = docid ? ` ${c.dim}#${docid}${c.reset}` : "";
      console.log(`${c.cyan}${path}${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}`);
      console.log();

      // Snippet with highlighting (no leading | chars for better word wrap)
      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 (const row of filtered) {
      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).snippet;
      if (opts.lineNumbers) {
        content = addLineNumbers(content);
      }
      const docidLine = docid ? `\n**docid:** \`#${docid}\`\n` : "";
      console.log(`---\n# ${heading}${docidLine}\n${content}\n`);
    }
  } else if (opts.format === "xml") {
    for (const row of filtered) {
      const titleAttr = row.title ? ` title="${row.title.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).snippet;
      if (opts.lineNumbers) {
        content = addLineNumbers(content);
      }
      console.log(`<file docid="#${docid}" name="${row.displayPath}"${titleAttr}>\n${content}\n</file>\n`);
    }
  } else {
    // CSV format
    console.log("docid,score,file,title,line,snippet");
    for (const row of filtered) {
      const { line, snippet } = extractSnippet(row.body, query, 500, row.chunkPos);
      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) : "");
      console.log(`#${docid},${row.score.toFixed(4)},${escapeCSV(row.displayPath)},${escapeCSV(row.title)},${line},${escapeCSV(content)}`);
    }
  }
}

function search(query: string, opts: OutputOptions): void {
  const db = getDb();

  // Validate collection filter if specified
  let collectionName: string | undefined;
  if (opts.collection) {
    const coll = getCollectionFromYaml(opts.collection);
    if (!coll) {
      console.error(`Collection not found: ${opts.collection}`);
      closeDb();
      process.exit(1);
    }
    collectionName = opts.collection;
  }

  // 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);
  // searchFTS accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
  const results = searchFTS(db, query, fetchLimit, collectionName as any);

  // Add context to results
  const resultsWithContext = results.map(r => ({
    ...r,
    context: getContextForFile(db, r.filepath),
  }));

  closeDb();

  if (resultsWithContext.length === 0) {
    console.log("No results found.");
    return;
  }
  outputResults(resultsWithContext, query, opts);
}

async function vectorSearch(query: string, opts: OutputOptions, model: string = DEFAULT_EMBED_MODEL): Promise<void> {
  const db = getDb();

  // Validate collection filter if specified
  let collectionName: string | undefined;
  if (opts.collection) {
    const coll = getCollectionFromYaml(opts.collection);
    if (!coll) {
      console.error(`Collection not found: ${opts.collection}`);
      closeDb();
      process.exit(1);
    }
    collectionName = opts.collection;
  }

  const tableExists = db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();
  if (!tableExists) {
    console.error("Vector index not found. Run 'qmd embed' first to create embeddings.");
    closeDb();
    return;
  }

  // Check index health and warn about issues
  checkIndexHealth(db);

  // Expand query to multiple variations (with caching)
  const queries = await expandQuery(query, DEFAULT_QUERY_MODEL, db);
  process.stderr.write(`Searching with ${queries.length} query variations...\n`);

  // Collect results from all query variations
  // For --all, fetch more results per query
  const perQueryLimit = opts.all ? 500 : 20;
  const allResults = new Map<string, { file: string; displayPath: string; title: string; body: string; score: number }>();

  for (const q of queries) {
    // searchVec accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
    const vecResults = await searchVec(db, q, model, perQueryLimit, collectionName as any);
    for (const r of vecResults) {
      const existing = allResults.get(r.filepath);
      if (!existing || r.score > existing.score) {
        allResults.set(r.filepath, { file: r.filepath, displayPath: r.displayPath, title: r.title, body: r.body || "", score: r.score });
      }
    }
  }

  // Sort by max score and limit to requested count
  const results = Array.from(allResults.values())
    .sort((a, b) => b.score - a.score)
    .slice(0, opts.limit)
    .map(r => ({ ...r, context: getContextForFile(db, r.file) }));

  closeDb();

  if (results.length === 0) {
    console.log("No results found.");
    return;
  }
  outputResults(results, query, { ...opts, limit: results.length }); // Already limited
}

async function expandQuery(query: string, model: string = DEFAULT_QUERY_MODEL, db?: Database): Promise<string[]> {
  process.stderr.write("Generating query variations...\n");

  const prompt = `You are a search query expander. Given a search query, generate 2 alternative queries that would help find relevant documents.

Rules:
- Use synonyms and related terminology (e.g., "craft" → "craftsmanship", "quality", "excellence")
- Rephrase to capture different angles (e.g., "engineering culture" → "technical excellence", "developer practices")
- Keep proper nouns and named concepts exactly as written (e.g., "Build a Business", "Stripe", "Shopify")
- Each variation should be 3-8 words, natural search terms
- Do NOT just append words like "search" or "find" or "documents"

Query: "${query}"

Output exactly 2 variations, one per line, no numbering or bullets:`;

  const requestBody = {
    model,
    prompt,
    stream: false,
    think: false,
    options: { num_predict: 150 },
  };

  // Check cache
  const cacheDb = db || getDb();
  const cacheKey = getCacheKey(`${OLLAMA_URL}/api/generate`, requestBody);
  const cached = getCachedResult(cacheDb, cacheKey);

  let responseText: string;
  if (cached) {
    responseText = cached;
  } else {
    const response = await fetch(`${OLLAMA_URL}/api/generate`, {
      method: "POST",
      headers: { "Content-Type": "application/json" },
      body: JSON.stringify(requestBody),
    });

    if (!response.ok) {
      const errorText = await response.text();
      if (errorText.includes("not found") || errorText.includes("does not exist")) {
        await ensureModelAvailable(model);
        if (!db) cacheDb.close();
        return expandQuery(query, model, db);
      }
      if (!db) cacheDb.close();
      return [query];
    }

    const data = await response.json() as { response: string };
    responseText = data.response;
    setCachedResult(cacheDb, cacheKey, responseText);
  }

  if (!db) cacheDb.close();

  const lines = responseText.trim().split('\n')
    .map(l => l.replace(/^[\d\.\-\*\"\s]+/, '').replace(/["\s]+$/, '').trim())
    .filter(l => l.length > 2 && l.length < 100 && !l.startsWith('<') && !l.toLowerCase().includes('variation'))
    .slice(0, 2);

  const allQueries = [query, ...lines];
  process.stderr.write(`${c.dim}Queries: ${allQueries.join(' | ')}${c.reset}\n`);
  return allQueries;
}

async function querySearch(query: string, opts: OutputOptions, embedModel: string = DEFAULT_EMBED_MODEL, rerankModel: string = DEFAULT_RERANK_MODEL): Promise<void> {
  const db = getDb();

  // Validate collection filter if specified
  let collectionName: string | undefined;
  if (opts.collection) {
    const coll = getCollectionFromYaml(opts.collection);
    if (!coll) {
      console.error(`Collection not found: ${opts.collection}`);
      closeDb();
      process.exit(1);
    }
    collectionName = opts.collection;
  }

  // Check index health and warn about issues
  checkIndexHealth(db);

  // Expand query to multiple variations (with caching)
  const queries = await expandQuery(query, DEFAULT_QUERY_MODEL, db);
  process.stderr.write(`Searching with ${queries.length} query variations...\n`);

  // Collect ranked result lists for RRF fusion
  const rankedLists: RankedResult[][] = [];
  const hasVectors = !!db.prepare(`SELECT name FROM sqlite_master WHERE type='table' AND name='vectors_vec'`).get();

  for (const q of queries) {
    // FTS search - get ranked results
    // searchFTS accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
    const ftsResults = searchFTS(db, q, 20, collectionName as any);
    if (ftsResults.length > 0) {
      rankedLists.push(ftsResults.map(r => ({ file: r.filepath, displayPath: r.displayPath, title: r.title, body: r.body || "", score: r.score })));
    }

    // Vector search - get ranked results
    if (hasVectors) {
      // searchVec accepts collection name as number parameter for legacy reasons (will be fixed in store.ts)
      const vecResults = await searchVec(db, q, embedModel, 20, collectionName as any);
      if (vecResults.length > 0) {
        rankedLists.push(vecResults.map(r => ({ file: r.filepath, displayPath: r.displayPath, title: r.title, body: r.body || "", score: r.score })));
      }
    }
  }

  // Apply Reciprocal Rank Fusion to combine all ranked lists
  // Give 2x weight to original query results (first 2 lists: FTS + vector)
  const weights = rankedLists.map((_, i) => i < 2 ? 2.0 : 1.0);
  const fused = reciprocalRankFusion(rankedLists, weights);
  const candidates = fused.slice(0, 30); // Over-retrieve for reranking

  if (candidates.length === 0) {
    console.log("No results found.");
    closeDb();
    return;
  }

  // Rerank with the original query (with caching)
  const reranked = await rerank(
    query,
    candidates.map(c => ({ file: c.file, text: c.body })),
    rerankModel,
    db
  );

  // Blend RRF position score with reranker score using position-aware weights
  // Top retrieval results get more protection from reranker disagreement
  const candidateMap = new Map(candidates.map(c => [c.file, { displayPath: c.displayPath, title: c.title, body: c.body }]));
  const rrfRankMap = new Map(candidates.map((c, i) => [c.file, i + 1])); // 1-indexed rank

  const finalResults = reranked.map(r => {
    const rrfRank = rrfRankMap.get(r.file) || 30;
    // Position-aware blending: top retrieval results preserved more
    // Rank 1-3: 75% RRF, 25% reranker (trust retrieval for exact matches)
    // Rank 4-10: 60% RRF, 40% reranker
    // Rank 11+: 40% RRF, 60% reranker (trust reranker for lower-ranked)
    let rrfWeight: number;
    if (rrfRank <= 3) {
      rrfWeight = 0.75;
    } else if (rrfRank <= 10) {
      rrfWeight = 0.60;
    } else {
      rrfWeight = 0.40;
    }
    const rrfScore = 1 / rrfRank;  // Position-based: 1, 0.5, 0.33...
    const blendedScore = rrfWeight * rrfScore + (1 - rrfWeight) * r.score;
    const candidate = candidateMap.get(r.file);
    return {
      file: r.file,
      displayPath: candidate?.displayPath || "",
      title: candidate?.title || "",
      body: candidate?.body || "",
      score: blendedScore,
      context: getContextForFile(db, r.file),
    };
  }).sort((a, b) => b.score - a.score);

  closeDb();
  outputResults(finalResults, query, opts);
}

// Parse CLI arguments using util.parseArgs
function parseCLI() {
  const { values, positionals } = parseArgs({
    args: Bun.argv.slice(2), // Skip bun and script path
    options: {
      // Global options
      index: { type: "string" },
      help: { type: "boolean", short: "h" },
      // 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" },
      collection: { type: "string", short: "c" },  // Filter by collection
      // Collection options
      name: { type: "string" },  // collection name
      mask: { type: "string" },  // glob pattern
      // Embed options
      force: { type: "boolean", short: "f" },
      // Update options
      pull: { type: "boolean" },  // git pull before update
      // 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
    },
    allowPositionals: true,
    strict: false, // Allow unknown options to pass through
  });

  // Set global index name in store
  if (values.index) {
    setCustomIndexName(values.index);
  }

  // Determine output format
  let format: OutputFormat = "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 || false;

  const opts: OutputOptions = {
    format,
    full: values.full || false,
    limit: isAll ? 100000 : (values.n ? parseInt(values.n, 10) || defaultLimit : defaultLimit),
    minScore: values["min-score"] ? parseFloat(values["min-score"]) || 0 : 0,
    all: isAll,
    collection: values.collection as string | undefined,
    lineNumbers: values["line-numbers"] || false,
  };

  return {
    command: positionals[0] || "",
    args: positionals.slice(1),
    query: positionals.slice(1).join(" "),
    opts,
    values,
  };
}

function showHelp(): void {
  console.log("Usage:");
  console.log("  qmd collection add [path] --name <name> --mask <pattern>  - Create/index collection");
  console.log("  qmd collection list           - List all collections with details");
  console.log("  qmd collection remove <name>  - Remove a collection by name");
  console.log("  qmd collection rename <old> <new>  - Rename a collection");
  console.log("  qmd ls [collection[/path]]    - List collections or files in a collection");
  console.log("  qmd context add [path] \"text\" - Add context for path (defaults to current dir)");
  console.log("  qmd context list              - List all contexts");
  console.log("  qmd context rm <path>         - Remove context");
  console.log("  qmd get <file>[:line] [-l N] [--from N]  - Get document (optionally from line, max N lines)");
  console.log("  qmd multi-get <pattern> [-l N] [--max-bytes N]  - Get multiple docs by glob or comma-separated list");
  console.log("  qmd status                    - Show index status and collections");
  console.log("  qmd update [--pull]           - Re-index all collections (--pull: git pull first)");
  console.log("  qmd embed [-f]                - Create vector embeddings (chunks ~6KB each)");
  console.log("  qmd cleanup                   - Remove cache and orphaned data, vacuum DB");
  console.log("  qmd search <query>            - Full-text search (BM25)");
  console.log("  qmd vsearch <query>           - Vector similarity search");
  console.log("  qmd query <query>             - Combined search with query expansion + reranking");
  console.log("  qmd mcp                       - Start MCP server (for AI agent integration)");
  console.log("");
  console.log("Global options:");
  console.log("  --index <name>             - Use custom index name (default: index)");
  console.log("");
  console.log("Search options:");
  console.log("  -n <num>                   - Number of results (default: 5, or 20 for --files)");
  console.log("  --all                      - Return all matches (use with --min-score to filter)");
  console.log("  --min-score <num>          - Minimum similarity score");
  console.log("  --full                     - Output full document instead of snippet");
  console.log("  --line-numbers             - Add line numbers to output");
  console.log("  --files                    - Output docid,score,filepath,context (default: 20 results)");
  console.log("  --json                     - JSON output with snippets (default: 20 results)");
  console.log("  --csv                      - CSV output with snippets");
  console.log("  --md                       - Markdown output");
  console.log("  --xml                      - XML output");
  console.log("  -c, --collection <name>    - Filter results to a specific collection");
  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 - Output format (same as search)");
  console.log("");
  console.log("Environment:");
  console.log("  OLLAMA_URL                 - Ollama server URL (default: http://localhost:11434)");
  console.log("");
  console.log("Models:");
  console.log(`  Embedding: ${DEFAULT_EMBED_MODEL}`);
  console.log(`  Reranking: ${DEFAULT_RERANK_MODEL}`);
  console.log("");
  console.log(`Index: ${getDbPath()}`);
}

// Main CLI - only run if this is the main module
if (import.meta.main) {
const cli = parseCLI();

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|check|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 check               - Check for missing 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: string | undefined;
        let contextText: string;

        // 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 "check": {
        contextCheck();
        break;
      }

      case "rm":
      case "remove": {
        if (cli.args.length < 2) {
          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, check, rm");
        process.exit(1);
    }
    break;
  }

  // Legacy alias for backwards compatibility
  case "add-context": {
    console.error(`${c.yellow}Note: 'qmd add-context' is deprecated. Use 'qmd context add' instead.${c.reset}`);
    if (cli.args.length === 0) {
      console.error("Usage: qmd context add [path] \"text\"");
      process.exit(1);
    }
    let pathArg: string | undefined;
    let contextText: string;
    if (cli.args.length === 1) {
      pathArg = undefined;
      contextText = cli.args[0];
    } else {
      pathArg = cli.args[0];
      contextText = cli.args.slice(1).join(" ");
    }
    await contextAdd(pathArg, contextText);
    break;
  }

  case "get": {
    if (!cli.args[0]) {
      console.error("Usage: qmd get <filepath>[:line] [--from <line>] [-l <lines>]");
      process.exit(1);
    }
    const fromLine = cli.values.from ? parseInt(cli.values.from as string, 10) : undefined;
    const maxLines = cli.values.l ? parseInt(cli.values.l as string, 10) : undefined;
    getDocument(cli.args[0], fromLine, maxLines);
    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 as string, 10) : undefined;
    const maxBytes = cli.values["max-bytes"] ? parseInt(cli.values["max-bytes"] as string, 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 as string || DEFAULT_GLOB;
        const name = cli.values.name as string | undefined;

        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;
      }

      default:
        console.error(`Unknown subcommand: ${subcommand}`);
        console.error("Available: list, add, remove, rename");
        process.exit(1);
    }
    break;
  }

  case "status":
    showStatus();
    break;

  case "update":
    await updateCollections();
    break;

  case "embed":
    await vectorIndex(DEFAULT_EMBED_MODEL, cli.values.force || false);
    break;

  case "search":
    if (!cli.query) {
      console.error("Usage: qmd search [options] <query>");
      process.exit(1);
    }
    search(cli.query, cli.opts);
    break;

  case "vsearch":
    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":
    if (!cli.query) {
      console.error("Usage: qmd query [options] <query>");
      process.exit(1);
    }
    await querySearch(cli.query, cli.opts);
    break;

  case "mcp": {
    const { startMcpServer } = await import("./mcp.js");
    await startMcpServer();
    break;
  }

  case "cleanup": {
    const db = getDb();

    // 1. Clear ollama_cache
    const cacheCount = deleteOllamaCache(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);
}
} // end if (import.meta.main)