@colbymchenry/codegraph 0.8.0 → 0.9.0

package/dist/bin/codegraph.js

@@ -1,1257 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * CodeGraph CLI
- *
- * Command-line interface for CodeGraph code intelligence.
- *
- * Usage:
- *   codegraph                    Run interactive installer (when no args)
- *   codegraph install            Run interactive installer
- *   codegraph init [path]        Initialize CodeGraph in a project
- *   codegraph uninit [path]      Remove CodeGraph from a project
- *   codegraph index [path]       Index all files in the project
- *   codegraph sync [path]        Sync changes since last index
- *   codegraph status [path]      Show index status
- *   codegraph query <search>     Search for symbols
- *   codegraph files [options]    Show project file structure
- *   codegraph context <task>     Build context for a task
- *   codegraph affected [files]   Find test files affected by changes
- */
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-const commander_1 = require("commander");
-const path = __importStar(require("path"));
-const fs = __importStar(require("fs"));
-const directory_1 = require("../directory");
-const shimmer_progress_1 = require("../ui/shimmer-progress");
-const glyphs_1 = require("../ui/glyphs");
-const node_version_check_1 = require("./node-version-check");
-// Lazy-load heavy modules (CodeGraph, runInstaller) to keep CLI startup fast.
-async function loadCodeGraph() {
-    try {
-        return await Promise.resolve().then(() => __importStar(require('../index')));
-    }
-    catch (err) {
-        const msg = err instanceof Error ? err.message : String(err);
-        console.error(`\x1b[31m${(0, glyphs_1.getGlyphs)().err}\x1b[0m Failed to load CodeGraph modules.`);
-        console.error(`\n  Node: ${process.version}  Platform: ${process.platform} ${process.arch}`);
-        console.error(`\n  Error: ${msg}`);
-        console.error('\n  Try reinstalling with: npm install -g @colbymchenry/codegraph\n');
-        process.exit(1);
-    }
-}
-// Dynamic import helper — tsc compiles import() to require() in CJS mode,
-// which fails for ESM-only packages. This bypasses the transformation.
-// eslint-disable-next-line @typescript-eslint/no-implied-eval
-const importESM = new Function('specifier', 'return import(specifier)');
-// Block CodeGraph on Node.js 25.x — V8's turboshaft WASM JIT has a Zone
-// allocator bug that reliably crashes when compiling tree-sitter
-// grammars (see #54, #81, #140). The previous behaviour was a soft
-// console.warn that scrolls off-screen before the OOM crash 30 seconds
-// later, leading to a steady stream of "what is this OOM" reports.
-// Hard-exit before any WASM work; allow override via env var for users
-// who patched V8 themselves or want to test a future fix.
-const nodeVersion = process.versions.node;
-const nodeMajor = parseInt(nodeVersion.split('.')[0] ?? '0', 10);
-if (nodeMajor >= 25) {
-    process.stderr.write((0, node_version_check_1.buildNode25BlockBanner)(nodeVersion) + '\n');
-    if (!process.env.CODEGRAPH_ALLOW_UNSAFE_NODE) {
-        process.exit(1);
-    }
-    // Override active — banner shown for visibility, continuing.
-}
-// Check if running with no arguments - run installer
-if (process.argv.length === 2) {
-    Promise.resolve().then(() => __importStar(require('../installer'))).then(({ runInstaller }) => runInstaller()).catch((err) => {
-        console.error('Installation failed:', err instanceof Error ? err.message : String(err));
-        process.exit(1);
-    });
-}
-else {
-    // Normal CLI flow
-    main();
-}
-process.on('uncaughtException', (error) => {
-    console.error('[CodeGraph] Uncaught exception:', error);
-});
-process.on('unhandledRejection', (reason) => {
-    console.error('[CodeGraph] Unhandled rejection:', reason);
-});
-function main() {
-    const program = new commander_1.Command();
-    // Version from package.json
-    const packageJson = JSON.parse(fs.readFileSync(path.join(__dirname, '..', '..', 'package.json'), 'utf-8'));
-    // =============================================================================
-    // ANSI Color Helpers (avoid chalk ESM issues)
-    // =============================================================================
-    const colors = {
-        reset: '\x1b[0m',
-        bold: '\x1b[1m',
-        dim: '\x1b[2m',
-        red: '\x1b[31m',
-        green: '\x1b[32m',
-        yellow: '\x1b[33m',
-        blue: '\x1b[34m',
-        cyan: '\x1b[36m',
-        white: '\x1b[37m',
-        gray: '\x1b[90m',
-    };
-    const chalk = {
-        bold: (s) => `${colors.bold}${s}${colors.reset}`,
-        dim: (s) => `${colors.dim}${s}${colors.reset}`,
-        red: (s) => `${colors.red}${s}${colors.reset}`,
-        green: (s) => `${colors.green}${s}${colors.reset}`,
-        yellow: (s) => `${colors.yellow}${s}${colors.reset}`,
-        blue: (s) => `${colors.blue}${s}${colors.reset}`,
-        cyan: (s) => `${colors.cyan}${s}${colors.reset}`,
-        white: (s) => `${colors.white}${s}${colors.reset}`,
-        gray: (s) => `${colors.gray}${s}${colors.reset}`,
-    };
-    program
-        .name('codegraph')
-        .description('Code intelligence and knowledge graph for any codebase')
-        .version(packageJson.version);
-    // =============================================================================
-    // Helper Functions
-    // =============================================================================
-    /**
-     * Resolve project path from argument or current directory
-     * Walks up parent directories to find nearest initialized CodeGraph project
-     * (must have .codegraph/codegraph.db, not just .codegraph/lessons.db)
-     */
-    function resolveProjectPath(pathArg) {
-        const absolutePath = path.resolve(pathArg || process.cwd());
-        // If exact path is initialized (has codegraph.db), use it
-        if ((0, directory_1.isInitialized)(absolutePath)) {
-            return absolutePath;
-        }
-        // Walk up to find nearest parent with CodeGraph initialized
-        // Note: findNearestCodeGraphRoot finds any .codegraph folder, but we need one with codegraph.db
-        let current = absolutePath;
-        const root = path.parse(current).root;
-        while (current !== root) {
-            const parent = path.dirname(current);
-            if (parent === current)
-                break;
-            current = parent;
-            if ((0, directory_1.isInitialized)(current)) {
-                return current;
-            }
-        }
-        // Not found - return original path (will fail later with helpful error)
-        return absolutePath;
-    }
-    /**
-     * Format a number with commas
-     */
-    function formatNumber(n) {
-        return n.toLocaleString();
-    }
-    /**
-     * Format duration in milliseconds to human readable
-     */
-    function formatDuration(ms) {
-        if (ms < 1000) {
-            return `${ms}ms`;
-        }
-        const seconds = ms / 1000;
-        if (seconds < 60) {
-            return `${seconds.toFixed(1)}s`;
-        }
-        const minutes = Math.floor(seconds / 60);
-        const remainingSeconds = seconds % 60;
-        return `${minutes}m ${remainingSeconds.toFixed(0)}s`;
-    }
-    // Shimmer progress renderer (runs in a worker thread for smooth animation)
-    // Imported at top of file from '../ui/shimmer-progress'
-    /**
-     * Create a plain-text progress callback for --verbose mode.
-     * No animations, no ANSI tricks — just timestamped lines to stdout.
-     */
-    function createVerboseProgress() {
-        let lastPhase = '';
-        let lastPct = -1;
-        const startTime = Date.now();
-        return (progress) => {
-            const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
-            if (progress.phase !== lastPhase) {
-                lastPhase = progress.phase;
-                lastPct = -1;
-                console.log(`[${elapsed}s] Phase: ${progress.phase}`);
-            }
-            if (progress.total > 0) {
-                const pct = Math.floor((progress.current / progress.total) * 100);
-                // Log every 5% to keep output manageable
-                if (pct >= lastPct + 5 || progress.current === progress.total) {
-                    lastPct = pct;
-                    console.log(`[${elapsed}s]   ${progress.current}/${progress.total} (${pct}%)${progress.currentFile ? ` ${(0, glyphs_1.getGlyphs)().dash} ${progress.currentFile}` : ''}`);
-                }
-            }
-            else if (progress.current > 0) {
-                // Scanning phase (no total yet) — log periodically
-                if (progress.current % 1000 === 0 || progress.current === 1) {
-                    console.log(`[${elapsed}s]   ${formatNumber(progress.current)} files found`);
-                }
-            }
-        };
-    }
-    /**
-     * Print success message
-     */
-    function success(message) {
-        console.log(chalk.green((0, glyphs_1.getGlyphs)().ok) + ' ' + message);
-    }
-    /**
-     * Print error message
-     */
-    function error(message) {
-        console.error(chalk.red((0, glyphs_1.getGlyphs)().err) + ' ' + message);
-    }
-    /**
-     * Print info message
-     */
-    function info(message) {
-        console.log(chalk.blue((0, glyphs_1.getGlyphs)().info) + ' ' + message);
-    }
-    /**
-     * Print warning message
-     */
-    function warn(message) {
-        console.log(chalk.yellow((0, glyphs_1.getGlyphs)().warn) + ' ' + message);
-    }
-    /**
-     * Print indexing results using clack log methods
-     */
-    function printIndexResult(clack, result, projectPath) {
-        const hasErrors = result.filesErrored > 0;
-        // Surface non-file-level failures (e.g. lock-acquisition failure
-        // when another indexer is running) before the file-count branches.
-        // Without this the CLI falls through to "No files found to index",
-        // which is actively misleading — the index DID run, it just couldn't
-        // get the lock.
-        //
-        // If success is false but no severity:'error' entry exists in
-        // `result.errors` (degenerate case — shouldn't happen in practice
-        // but worth guarding because the result shape is plumbed through
-        // multiple call sites), fall back to a generic message rather than
-        // continuing to the misleading "No files found" branch or throwing.
-        if (!result.success && !hasErrors && result.filesIndexed === 0) {
-            const generic = result.errors.find((e) => e.severity === 'error');
-            clack.log.error(generic?.message ?? `Indexing failed ${(0, glyphs_1.getGlyphs)().dash} no further details available`);
-            return;
-        }
-        if (result.filesIndexed > 0) {
-            if (hasErrors) {
-                clack.log.success(`Indexed ${formatNumber(result.filesIndexed)} files (${formatNumber(result.filesErrored)} could not be parsed)`);
-            }
-            else {
-                clack.log.success(`Indexed ${formatNumber(result.filesIndexed)} files`);
-            }
-            clack.log.info(`${formatNumber(result.nodesCreated)} nodes, ${formatNumber(result.edgesCreated)} edges in ${formatDuration(result.durationMs)}`);
-        }
-        else if (hasErrors) {
-            clack.log.error(`Indexing failed ${(0, glyphs_1.getGlyphs)().dash} all ${formatNumber(result.filesErrored)} files had errors`);
-        }
-        else {
-            clack.log.warn('No files found to index');
-        }
-        if (hasErrors) {
-            const errorsByCode = new Map();
-            for (const err of result.errors) {
-                if (err.severity === 'error') {
-                    const code = err.code || 'unknown';
-                    errorsByCode.set(code, (errorsByCode.get(code) || 0) + 1);
-                }
-            }
-            const codeLabels = {
-                parse_error: 'files failed to parse',
-                read_error: 'files could not be read',
-                size_exceeded: 'files exceeded size limit',
-                path_traversal: 'blocked paths',
-                unsupported_language: 'unsupported language',
-                parser_error: 'parser initialization failures',
-            };
-            const breakdown = Array.from(errorsByCode)
-                .map(([code, count]) => `${formatNumber(count)} ${codeLabels[code] || code}`)
-                .join('\n');
-            clack.note(breakdown, 'Error breakdown');
-            if (projectPath) {
-                writeErrorLog(projectPath, result.errors);
-                clack.log.info('See .codegraph/errors.log for details');
-            }
-            if (result.filesIndexed > 0) {
-                clack.log.info(`The index is fully usable ${(0, glyphs_1.getGlyphs)().dash} only the failed files are missing.`);
-            }
-        }
-        else if (projectPath) {
-            const logPath = path.join(projectPath, '.codegraph', 'errors.log');
-            if (fs.existsSync(logPath)) {
-                fs.unlinkSync(logPath);
-            }
-        }
-    }
-    /**
-     * Write detailed error log to .codegraph/errors.log
-     */
-    function writeErrorLog(projectPath, errors) {
-        const cgDir = path.join(projectPath, '.codegraph');
-        if (!fs.existsSync(cgDir))
-            return;
-        const logPath = path.join(cgDir, 'errors.log');
-        // Group errors by file path
-        const errorsByFile = new Map();
-        const noFileErrors = [];
-        for (const err of errors) {
-            if (err.severity !== 'error')
-                continue;
-            if (err.filePath) {
-                let list = errorsByFile.get(err.filePath);
-                if (!list) {
-                    list = [];
-                    errorsByFile.set(err.filePath, list);
-                }
-                list.push({ message: err.message, code: err.code });
-            }
-            else {
-                noFileErrors.push({ message: err.message, code: err.code });
-            }
-        }
-        const lines = [
-            `CodeGraph Error Log - ${new Date().toISOString()}`,
-            `${errorsByFile.size} files with errors`,
-            '',
-        ];
-        for (const [filePath, fileErrors] of errorsByFile) {
-            for (const err of fileErrors) {
-                lines.push(`${filePath}: ${err.message}`);
-            }
-        }
-        for (const err of noFileErrors) {
-            lines.push(err.message);
-        }
-        fs.writeFileSync(logPath, lines.join('\n') + '\n');
-    }
-    // =============================================================================
-    // Commands
-    // =============================================================================
-    /**
-     * codegraph init [path]
-     */
-    program
-        .command('init [path]')
-        .description('Initialize CodeGraph in a project directory')
-        .option('-i, --index', 'Run initial indexing after initialization')
-        .option('-v, --verbose', 'Show detailed worker lifecycle and memory info')
-        .action(async (pathArg, options) => {
-        const projectPath = path.resolve(pathArg || process.cwd());
-        const clack = await importESM('@clack/prompts');
-        clack.intro('Initializing CodeGraph');
-        try {
-            if ((0, directory_1.isInitialized)(projectPath)) {
-                clack.log.warn(`Already initialized in ${projectPath}`);
-                clack.log.info('Use "codegraph index" to re-index or "codegraph sync" to update');
-                // Re-run agent surface wiring so re-running `init` is the
-                // documented way to recover a project that's missing its
-                // Cursor rules file (or future per-agent project surfaces).
-                try {
-                    const { wireProjectSurfacesForGlobalAgents } = await Promise.resolve().then(() => __importStar(require('../installer')));
-                    for (const { target, file } of wireProjectSurfacesForGlobalAgents()) {
-                        clack.log.success(`${target.displayName}: ${file.action} ${file.path}`);
-                    }
-                }
-                catch { /* non-fatal */ }
-                try {
-                    const { offerWatchFallback } = await Promise.resolve().then(() => __importStar(require('../installer')));
-                    await offerWatchFallback(clack, projectPath);
-                }
-                catch { /* non-fatal */ }
-                clack.outro('');
-                return;
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.init(projectPath, { index: false });
-            clack.log.success(`Initialized in ${projectPath}`);
-            // Bootstrap project-local surfaces for any agent that's
-            // configured globally (Cursor needs ./.cursor/rules/codegraph.mdc
-            // to actually prefer codegraph over native grep). Silent when
-            // there's nothing to write.
-            try {
-                const { wireProjectSurfacesForGlobalAgents } = await Promise.resolve().then(() => __importStar(require('../installer')));
-                for (const { target, file } of wireProjectSurfacesForGlobalAgents()) {
-                    clack.log.success(`${target.displayName}: ${file.action} ${file.path}`);
-                }
-            }
-            catch (err) {
-                const msg = err instanceof Error ? err.message : String(err);
-                clack.log.warn(`Skipped wiring project-local agent surfaces: ${msg}`);
-            }
-            if (options.index) {
-                let result;
-                if (options.verbose) {
-                    result = await cg.indexAll({
-                        onProgress: createVerboseProgress(),
-                        verbose: true,
-                    });
-                }
-                else {
-                    process.stdout.write(`${colors.dim}${(0, glyphs_1.getGlyphs)().rail}${colors.reset}\n`);
-                    const progress = (0, shimmer_progress_1.createShimmerProgress)();
-                    result = await cg.indexAll({
-                        onProgress: progress.onProgress,
-                    });
-                    await progress.stop();
-                }
-                printIndexResult(clack, result, projectPath);
-            }
-            else {
-                clack.log.info('Run "codegraph index" to index the project');
-            }
-            try {
-                const { offerWatchFallback } = await Promise.resolve().then(() => __importStar(require('../installer')));
-                await offerWatchFallback(clack, projectPath);
-            }
-            catch { /* non-fatal */ }
-            clack.outro('Done');
-            cg.destroy();
-        }
-        catch (err) {
-            clack.log.error(`Failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph uninit [path]
-     */
-    program
-        .command('uninit [path]')
-        .description('Remove CodeGraph from a project (deletes .codegraph/ directory)')
-        .option('-f, --force', 'Skip confirmation prompt')
-        .action(async (pathArg, options) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                warn(`CodeGraph is not initialized in ${projectPath}`);
-                return;
-            }
-            if (!options.force) {
-                // Confirm with user
-                const readline = await Promise.resolve().then(() => __importStar(require('readline')));
-                const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
-                const answer = await new Promise((resolve) => {
-                    rl.question(chalk.yellow(`${(0, glyphs_1.getGlyphs)().warn} This will permanently delete all CodeGraph data. Continue? (y/N) `), resolve);
-                });
-                rl.close();
-                if (answer.toLowerCase() !== 'y') {
-                    info('Cancelled');
-                    return;
-                }
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = CodeGraph.openSync(projectPath);
-            cg.uninitialize();
-            // Clean up any git sync hooks we installed (no-op if none / not a repo).
-            try {
-                const { removeGitSyncHook } = await Promise.resolve().then(() => __importStar(require('../sync/git-hooks')));
-                const removed = removeGitSyncHook(projectPath);
-                if (removed.installed.length > 0) {
-                    info(`Removed git ${removed.installed.join(', ')} sync hook${removed.installed.length > 1 ? 's' : ''}`);
-                }
-            }
-            catch { /* non-fatal */ }
-            success(`Removed CodeGraph from ${projectPath}`);
-        }
-        catch (err) {
-            error(`Failed to uninitialize: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph index [path]
-     */
-    program
-        .command('index [path]')
-        .description('Index all files in the project')
-        .option('-f, --force', 'Force full re-index even if already indexed')
-        .option('-q, --quiet', 'Suppress progress output')
-        .option('-v, --verbose', 'Show detailed worker lifecycle and memory info')
-        .action(async (pathArg, options) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                info('Run "codegraph init" first');
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            if (options.quiet) {
-                // Quiet mode: no UI, just run
-                if (options.force)
-                    cg.clear();
-                const result = await cg.indexAll();
-                if (!result.success)
-                    process.exit(1);
-                cg.destroy();
-                return;
-            }
-            const clack = await importESM('@clack/prompts');
-            clack.intro('Indexing project');
-            if (options.force) {
-                cg.clear();
-                clack.log.info('Cleared existing index');
-            }
-            let result;
-            if (options.verbose) {
-                result = await cg.indexAll({
-                    onProgress: createVerboseProgress(),
-                    verbose: true,
-                });
-            }
-            else {
-                process.stdout.write(`${colors.dim}${(0, glyphs_1.getGlyphs)().rail}${colors.reset}\n`);
-                const progress = (0, shimmer_progress_1.createShimmerProgress)();
-                result = await cg.indexAll({
-                    onProgress: progress.onProgress,
-                });
-                await progress.stop();
-            }
-            printIndexResult(clack, result, projectPath);
-            if (!result.success) {
-                process.exit(1);
-            }
-            clack.outro('Done');
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Failed to index: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph sync [path]
-     */
-    program
-        .command('sync [path]')
-        .description('Sync changes since last index')
-        .option('-q, --quiet', 'Suppress output (for git hooks)')
-        .action(async (pathArg, options) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                if (!options.quiet) {
-                    error(`CodeGraph not initialized in ${projectPath}`);
-                }
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            if (options.quiet) {
-                await cg.sync();
-                cg.destroy();
-                return;
-            }
-            const clack = await importESM('@clack/prompts');
-            clack.intro('Syncing CodeGraph');
-            process.stdout.write(`${colors.dim}${(0, glyphs_1.getGlyphs)().rail}${colors.reset}\n`);
-            const progress = (0, shimmer_progress_1.createShimmerProgress)();
-            const result = await cg.sync({
-                onProgress: progress.onProgress,
-            });
-            await progress.stop();
-            const totalChanges = result.filesAdded + result.filesModified + result.filesRemoved;
-            if (totalChanges === 0) {
-                clack.log.info('Already up to date');
-            }
-            else {
-                clack.log.success(`Synced ${formatNumber(totalChanges)} changed files`);
-                const details = [];
-                if (result.filesAdded > 0)
-                    details.push(`Added: ${result.filesAdded}`);
-                if (result.filesModified > 0)
-                    details.push(`Modified: ${result.filesModified}`);
-                if (result.filesRemoved > 0)
-                    details.push(`Removed: ${result.filesRemoved}`);
-                clack.log.info(`${details.join(', ')} ${(0, glyphs_1.getGlyphs)().dash} ${formatNumber(result.nodesUpdated)} nodes in ${formatDuration(result.durationMs)}`);
-            }
-            clack.outro('Done');
-            cg.destroy();
-        }
-        catch (err) {
-            if (!options.quiet) {
-                error(`Failed to sync: ${err instanceof Error ? err.message : String(err)}`);
-            }
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph status [path]
-     */
-    program
-        .command('status [path]')
-        .description('Show index status and statistics')
-        .option('-j, --json', 'Output as JSON')
-        .action(async (pathArg, options) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                if (options.json) {
-                    console.log(JSON.stringify({ initialized: false, projectPath }));
-                    return;
-                }
-                console.log(chalk.bold('\nCodeGraph Status\n'));
-                info(`Project: ${projectPath}`);
-                warn('Not initialized');
-                info('Run "codegraph init" to initialize');
-                return;
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const stats = cg.getStats();
-            const changes = cg.getChangedFiles();
-            const backend = cg.getBackend();
-            // JSON output mode
-            if (options.json) {
-                console.log(JSON.stringify({
-                    initialized: true,
-                    projectPath,
-                    fileCount: stats.fileCount,
-                    nodeCount: stats.nodeCount,
-                    edgeCount: stats.edgeCount,
-                    dbSizeBytes: stats.dbSizeBytes,
-                    backend,
-                    nodesByKind: stats.nodesByKind,
-                    languages: Object.entries(stats.filesByLanguage).filter(([, count]) => count > 0).map(([lang]) => lang),
-                    pendingChanges: {
-                        added: changes.added.length,
-                        modified: changes.modified.length,
-                        removed: changes.removed.length,
-                    },
-                }));
-                cg.destroy();
-                return;
-            }
-            console.log(chalk.bold('\nCodeGraph Status\n'));
-            // Project info
-            console.log(chalk.cyan('Project:'), projectPath);
-            console.log();
-            // Index stats
-            console.log(chalk.bold('Index Statistics:'));
-            console.log(`  Files:     ${formatNumber(stats.fileCount)}`);
-            console.log(`  Nodes:     ${formatNumber(stats.nodeCount)}`);
-            console.log(`  Edges:     ${formatNumber(stats.edgeCount)}`);
-            console.log(`  DB Size:   ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`);
-            // Surface the active SQLite backend so users can spot the silent
-            // WASM fallback (5-10x slower). better-sqlite3 is in
-            // `optionalDependencies`, so `npm install` succeeds without it
-            // when the native build fails.
-            const backendLabel = backend === 'native'
-                ? chalk.green('native')
-                : chalk.yellow(`wasm ${(0, glyphs_1.getGlyphs)().dash} slower fallback; run \`npm rebuild better-sqlite3\``);
-            console.log(`  Backend:   ${backendLabel}`);
-            console.log();
-            // Node breakdown
-            console.log(chalk.bold('Nodes by Kind:'));
-            const nodesByKind = Object.entries(stats.nodesByKind)
-                .filter(([, count]) => count > 0)
-                .sort((a, b) => b[1] - a[1]);
-            for (const [kind, count] of nodesByKind) {
-                console.log(`  ${kind.padEnd(15)} ${formatNumber(count)}`);
-            }
-            console.log();
-            // Language breakdown
-            console.log(chalk.bold('Files by Language:'));
-            const filesByLang = Object.entries(stats.filesByLanguage)
-                .filter(([, count]) => count > 0)
-                .sort((a, b) => b[1] - a[1]);
-            for (const [lang, count] of filesByLang) {
-                console.log(`  ${lang.padEnd(15)} ${formatNumber(count)}`);
-            }
-            console.log();
-            // Pending changes
-            const totalChanges = changes.added.length + changes.modified.length + changes.removed.length;
-            if (totalChanges > 0) {
-                console.log(chalk.bold('Pending Changes:'));
-                if (changes.added.length > 0) {
-                    console.log(`  Added:     ${changes.added.length} files`);
-                }
-                if (changes.modified.length > 0) {
-                    console.log(`  Modified:  ${changes.modified.length} files`);
-                }
-                if (changes.removed.length > 0) {
-                    console.log(`  Removed:   ${changes.removed.length} files`);
-                }
-                info('Run "codegraph sync" to update the index');
-            }
-            else {
-                success('Index is up to date');
-            }
-            console.log();
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Failed to get status: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph query <search>
-     */
-    program
-        .command('query <search>')
-        .description('Search for symbols in the codebase')
-        .option('-p, --path <path>', 'Project path')
-        .option('-l, --limit <number>', 'Maximum results', '10')
-        .option('-k, --kind <kind>', 'Filter by node kind (function, class, etc.)')
-        .option('-j, --json', 'Output as JSON')
-        .action(async (search, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const limit = parseInt(options.limit || '10', 10);
-            const results = cg.searchNodes(search, {
-                limit,
-                kinds: options.kind ? [options.kind] : undefined,
-            });
-            if (options.json) {
-                console.log(JSON.stringify(results, null, 2));
-            }
-            else {
-                if (results.length === 0) {
-                    info(`No results found for "${search}"`);
-                }
-                else {
-                    console.log(chalk.bold(`\nSearch Results for "${search}":\n`));
-                    for (const result of results) {
-                        const node = result.node;
-                        const location = `${node.filePath}:${node.startLine}`;
-                        const score = chalk.dim(`(${(result.score * 100).toFixed(0)}%)`);
-                        console.log(chalk.cyan(node.kind.padEnd(12)) +
-                            chalk.white(node.name) +
-                            ' ' + score);
-                        console.log(chalk.dim(`  ${location}`));
-                        if (node.signature) {
-                            console.log(chalk.dim(`  ${node.signature}`));
-                        }
-                        console.log();
-                    }
-                }
-            }
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Search failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph files [path]
-     */
-    program
-        .command('files')
-        .description('Show project file structure from the index')
-        .option('-p, --path <path>', 'Project path')
-        .option('--filter <dir>', 'Filter to files under this directory')
-        .option('--pattern <glob>', 'Filter files matching this glob pattern')
-        .option('--format <format>', 'Output format (tree, flat, grouped)', 'tree')
-        .option('--max-depth <number>', 'Maximum directory depth for tree format')
-        .option('--no-metadata', 'Hide file metadata (language, symbol count)')
-        .option('-j, --json', 'Output as JSON')
-        .action(async (options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            let files = cg.getFiles();
-            if (files.length === 0) {
-                info('No files indexed. Run "codegraph index" first.');
-                cg.destroy();
-                return;
-            }
-            // Filter by path prefix
-            if (options.filter) {
-                const filter = options.filter;
-                files = files.filter(f => f.path.startsWith(filter) || f.path.startsWith('./' + filter));
-            }
-            // Filter by glob pattern
-            if (options.pattern) {
-                const regex = globToRegex(options.pattern);
-                files = files.filter(f => regex.test(f.path));
-            }
-            if (files.length === 0) {
-                info('No files found matching the criteria.');
-                cg.destroy();
-                return;
-            }
-            // JSON output
-            if (options.json) {
-                const output = files.map(f => ({
-                    path: f.path,
-                    language: f.language,
-                    nodeCount: f.nodeCount,
-                    size: f.size,
-                }));
-                console.log(JSON.stringify(output, null, 2));
-                cg.destroy();
-                return;
-            }
-            const includeMetadata = options.metadata !== false;
-            const format = options.format || 'tree';
-            const maxDepth = options.maxDepth ? parseInt(options.maxDepth, 10) : undefined;
-            // Format output
-            switch (format) {
-                case 'flat':
-                    console.log(chalk.bold(`\nFiles (${files.length}):\n`));
-                    for (const file of files.sort((a, b) => a.path.localeCompare(b.path))) {
-                        if (includeMetadata) {
-                            console.log(`  ${file.path} ${chalk.dim(`(${file.language}, ${file.nodeCount} symbols)`)}`);
-                        }
-                        else {
-                            console.log(`  ${file.path}`);
-                        }
-                    }
-                    break;
-                case 'grouped':
-                    console.log(chalk.bold(`\nFiles by Language (${files.length} total):\n`));
-                    const byLang = new Map();
-                    for (const file of files) {
-                        const existing = byLang.get(file.language) || [];
-                        existing.push(file);
-                        byLang.set(file.language, existing);
-                    }
-                    const sortedLangs = [...byLang.entries()].sort((a, b) => b[1].length - a[1].length);
-                    for (const [lang, langFiles] of sortedLangs) {
-                        console.log(chalk.cyan(`${lang} (${langFiles.length}):`));
-                        for (const file of langFiles.sort((a, b) => a.path.localeCompare(b.path))) {
-                            if (includeMetadata) {
-                                console.log(`  ${file.path} ${chalk.dim(`(${file.nodeCount} symbols)`)}`);
-                            }
-                            else {
-                                console.log(`  ${file.path}`);
-                            }
-                        }
-                        console.log();
-                    }
-                    break;
-                case 'tree':
-                default:
-                    console.log(chalk.bold(`\nProject Structure (${files.length} files):\n`));
-                    printFileTree(files, includeMetadata, maxDepth, chalk);
-                    break;
-            }
-            console.log();
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Failed to list files: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * Convert glob pattern to regex
-     */
-    function globToRegex(pattern) {
-        const escaped = pattern
-            .replace(/[.+^${}()|[\]\\]/g, '\\$&')
-            .replace(/\*\*/g, '{{GLOBSTAR}}')
-            .replace(/\*/g, '[^/]*')
-            .replace(/\?/g, '[^/]')
-            .replace(/\{\{GLOBSTAR\}\}/g, '.*');
-        return new RegExp(escaped);
-    }
-    /**
-     * Print files as a tree
-     */
-    function printFileTree(files, includeMetadata, maxDepth, chalk) {
-        const root = { name: '', children: new Map() };
-        for (const file of files) {
-            const parts = file.path.split('/');
-            let current = root;
-            for (let i = 0; i < parts.length; i++) {
-                const part = parts[i];
-                if (!part)
-                    continue;
-                if (!current.children.has(part)) {
-                    current.children.set(part, { name: part, children: new Map() });
-                }
-                current = current.children.get(part);
-                if (i === parts.length - 1) {
-                    current.file = { language: file.language, nodeCount: file.nodeCount };
-                }
-            }
-        }
-        const renderNode = (node, prefix, isLast, depth) => {
-            if (maxDepth !== undefined && depth > maxDepth)
-                return;
-            const glyphs = (0, glyphs_1.getGlyphs)();
-            const connector = isLast ? glyphs.treeLast : glyphs.treeBranch;
-            const childPrefix = isLast ? '    ' : glyphs.treePipe;
-            if (node.name) {
-                let line = prefix + connector + node.name;
-                if (node.file && includeMetadata) {
-                    line += chalk.dim(` (${node.file.language}, ${node.file.nodeCount} symbols)`);
-                }
-                console.log(line);
-            }
-            const children = [...node.children.values()];
-            children.sort((a, b) => {
-                const aIsDir = a.children.size > 0 && !a.file;
-                const bIsDir = b.children.size > 0 && !b.file;
-                if (aIsDir !== bIsDir)
-                    return aIsDir ? -1 : 1;
-                return a.name.localeCompare(b.name);
-            });
-            for (let i = 0; i < children.length; i++) {
-                const child = children[i];
-                const nextPrefix = node.name ? prefix + childPrefix : prefix;
-                renderNode(child, nextPrefix, i === children.length - 1, depth + 1);
-            }
-        };
-        renderNode(root, '', true, 0);
-    }
-    /**
-     * codegraph context <task>
-     */
-    program
-        .command('context <task>')
-        .description('Build context for a task (outputs markdown)')
-        .option('-p, --path <path>', 'Project path')
-        .option('-n, --max-nodes <number>', 'Maximum nodes to include', '50')
-        .option('-c, --max-code <number>', 'Maximum code blocks', '10')
-        .option('--no-code', 'Exclude code blocks')
-        .option('-f, --format <format>', 'Output format (markdown, json)', 'markdown')
-        .action(async (task, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const context = await cg.buildContext(task, {
-                maxNodes: parseInt(options.maxNodes || '50', 10),
-                maxCodeBlocks: parseInt(options.maxCode || '10', 10),
-                includeCode: options.code !== false,
-                format: options.format,
-            });
-            // Output the context
-            console.log(context);
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Failed to build context: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph serve
-     */
-    program
-        .command('serve')
-        .description('Start CodeGraph as an MCP server for AI assistants')
-        .option('-p, --path <path>', 'Project path (optional for MCP mode, uses rootUri from client)')
-        .option('--mcp', 'Run as MCP server (stdio transport)')
-        .option('--no-watch', 'Disable the file watcher (no auto-sync; useful on slow filesystems like WSL2 /mnt drives)')
-        .action(async (options) => {
-        const projectPath = options.path ? resolveProjectPath(options.path) : undefined;
-        // Commander sets watch=false when --no-watch is passed. Route it through
-        // the same env-var chokepoint the watcher and MCP server already honor.
-        if (options.watch === false) {
-            process.env.CODEGRAPH_NO_WATCH = '1';
-        }
-        try {
-            if (options.mcp) {
-                // Start MCP server - it handles initialization lazily based on rootUri from client
-                const { MCPServer } = await Promise.resolve().then(() => __importStar(require('../mcp/index')));
-                const server = new MCPServer(projectPath);
-                await server.start();
-                // Server will run until terminated
-            }
-            else {
-                // Default: show info about MCP mode.
-                // Use stderr so stdout stays clean for any piped/stdio usage.
-                console.error(chalk.bold('\nCodeGraph MCP Server\n'));
-                console.error(chalk.blue((0, glyphs_1.getGlyphs)().info) + ' Use --mcp flag to start the MCP server');
-                console.error('\nTo use with Claude Code, add to your MCP configuration:');
-                console.error(chalk.dim(`
-{
-  "mcpServers": {
-    "codegraph": {
-      "command": "codegraph",
-      "args": ["serve", "--mcp"]
-    }
-  }
-}
-`));
-                console.error('Available tools:');
-                console.error(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
-                console.error(chalk.cyan('  codegraph_context') + '   - Build context for a task');
-                console.error(chalk.cyan('  codegraph_callers') + '   - Find callers of a symbol');
-                console.error(chalk.cyan('  codegraph_callees') + '   - Find what a symbol calls');
-                console.error(chalk.cyan('  codegraph_impact') + '    - Analyze impact of changes');
-                console.error(chalk.cyan('  codegraph_node') + '      - Get symbol details');
-                console.error(chalk.cyan('  codegraph_files') + '     - Get project file structure');
-                console.error(chalk.cyan('  codegraph_status') + '    - Get index status');
-            }
-        }
-        catch (err) {
-            error(`Failed to start server: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph unlock [path]
-     */
-    program
-        .command('unlock [path]')
-        .description('Remove a stale lock file that is blocking indexing')
-        .action(async (pathArg) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                return;
-            }
-            const lockPath = path.join((0, directory_1.getCodeGraphDir)(projectPath), 'codegraph.lock');
-            if (!fs.existsSync(lockPath)) {
-                info(`No lock file found ${(0, glyphs_1.getGlyphs)().dash} nothing to do`);
-                return;
-            }
-            fs.unlinkSync(lockPath);
-            success('Removed lock file. You can now run indexing again.');
-        }
-        catch (err) {
-            error(`Failed to remove lock: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph affected [files...]
-     *
-     * Find test files affected by the given source files.
-     * Traces dependency edges transitively to find test files that depend on changed code.
-     *
-     * Usage:
-     *   git diff --name-only | codegraph affected --stdin
-     *   codegraph affected src/lib/components/Editor.svelte src/routes/+page.svelte
-     */
-    program
-        .command('affected [files...]')
-        .description('Find test files affected by changed source files')
-        .option('-p, --path <path>', 'Project path')
-        .option('--stdin', 'Read file list from stdin (one per line)')
-        .option('-d, --depth <number>', 'Max dependency traversal depth', '5')
-        .option('-f, --filter <glob>', 'Custom glob filter for test files (e.g. "e2e/*.spec.ts")')
-        .option('-j, --json', 'Output as JSON')
-        .option('-q, --quiet', 'Only output file paths, no decoration')
-        .action(async (fileArgs, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`CodeGraph not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            // Collect changed files from args or stdin
-            let changedFiles = [...(fileArgs || [])];
-            if (options.stdin) {
-                const stdinData = fs.readFileSync(0, 'utf-8');
-                const stdinFiles = stdinData.split('\n').map(f => f.trim()).filter(Boolean);
-                changedFiles.push(...stdinFiles);
-            }
-            if (changedFiles.length === 0) {
-                if (!options.quiet)
-                    info('No files provided. Use file arguments or --stdin.');
-                process.exit(0);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const maxDepth = parseInt(options.depth || '5', 10);
-            // Common test file patterns
-            const defaultTestPatterns = [
-                /\.spec\./,
-                /\.test\./,
-                /\/__tests__\//,
-                /\/tests?\//,
-                /\/e2e\//,
-                /\/spec\//,
-            ];
-            // Custom filter pattern
-            let customFilter = null;
-            if (options.filter) {
-                // Convert glob to regex: ** → .+, * → [^/]*, . → \.
-                const regex = options.filter
-                    .replace(/[+[\]{}()^$|\\]/g, '\\$&')
-                    .replace(/\./g, '\\.')
-                    .replace(/\*\*/g, '.+')
-                    .replace(/\*/g, '[^/]*');
-                customFilter = new RegExp(regex);
-            }
-            function isTestFile(filePath) {
-                if (customFilter)
-                    return customFilter.test(filePath);
-                return defaultTestPatterns.some(p => p.test(filePath));
-            }
-            // BFS to find all transitive dependents of changed files, filtered to test files
-            const affectedTests = new Set();
-            const allDependents = new Set();
-            for (const file of changedFiles) {
-                // If the changed file is itself a test file, include it
-                if (isTestFile(file)) {
-                    affectedTests.add(file);
-                    continue;
-                }
-                // BFS through dependents
-                const queue = [{ file, depth: 0 }];
-                const visited = new Set();
-                visited.add(file);
-                while (queue.length > 0) {
-                    const current = queue.shift();
-                    if (current.depth >= maxDepth)
-                        continue;
-                    const dependents = cg.getFileDependents(current.file);
-                    for (const dep of dependents) {
-                        if (visited.has(dep))
-                            continue;
-                        visited.add(dep);
-                        allDependents.add(dep);
-                        if (isTestFile(dep)) {
-                            affectedTests.add(dep);
-                        }
-                        else {
-                            queue.push({ file: dep, depth: current.depth + 1 });
-                        }
-                    }
-                }
-            }
-            const sortedTests = Array.from(affectedTests).sort();
-            // Output
-            if (options.json) {
-                console.log(JSON.stringify({
-                    changedFiles,
-                    affectedTests: sortedTests,
-                    totalDependentsTraversed: allDependents.size,
-                }, null, 2));
-            }
-            else if (options.quiet) {
-                for (const t of sortedTests)
-                    console.log(t);
-            }
-            else {
-                if (sortedTests.length === 0) {
-                    info('No test files affected by the changed files.');
-                }
-                else {
-                    console.log(chalk.bold(`\nAffected test files (${sortedTests.length}):\n`));
-                    for (const t of sortedTests) {
-                        console.log('  ' + chalk.cyan(t));
-                    }
-                    console.log();
-                }
-            }
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Affected analysis failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * codegraph install
-     */
-    program
-        .command('install')
-        .description('Install codegraph MCP server into one or more agents (Claude Code, Cursor, Codex CLI, opencode)')
-        .option('-t, --target <ids>', 'Target agent(s): comma-separated ids, or "auto"|"all"|"none". Default: prompt')
-        .option('-l, --location <where>', 'Install location: "global" or "local". Default: prompt')
-        .option('-y, --yes', 'Non-interactive: defaults to --location=global --target=auto, auto-allow on')
-        .option('--no-permissions', 'Skip writing the auto-allow permissions list (Claude Code only)')
-        .option('--print-config <id>', 'Print MCP config snippet for the named agent and exit (no file writes)')
-        .action(async (opts) => {
-        if (opts.printConfig) {
-            const { getTarget, listTargetIds } = await Promise.resolve().then(() => __importStar(require('../installer/targets/registry')));
-            const target = getTarget(opts.printConfig);
-            if (!target) {
-                const known = listTargetIds().join(', ');
-                error(`Unknown target "${opts.printConfig}". Known: ${known}.`);
-                process.exit(1);
-            }
-            const loc = (opts.location === 'local' ? 'local' : 'global');
-            process.stdout.write(target.printConfig(loc));
-            return;
-        }
-        const { runInstallerWithOptions } = await Promise.resolve().then(() => __importStar(require('../installer')));
-        if (opts.location && opts.location !== 'global' && opts.location !== 'local') {
-            error(`--location must be "global" or "local" (got "${opts.location}").`);
-            process.exit(1);
-        }
-        try {
-            // Commander's `--no-permissions` makes `opts.permissions === false`;
-            // omitting the flag leaves it `true` (the positive-form default).
-            // We MUST treat the default-true as "user did not override — let
-            // the orchestrator prompt" and only forward an explicit `false`
-            // (or `true` when --yes implies it). Otherwise the auto-allow
-            // prompt is silently skipped on every interactive run.
-            const explicitNoPermissions = opts.permissions === false;
-            const autoAllow = explicitNoPermissions
-                ? false
-                : opts.yes
-                    ? true
-                    : undefined;
-            await runInstallerWithOptions({
-                target: opts.target,
-                location: opts.location,
-                autoAllow,
-                yes: opts.yes,
-            });
-        }
-        catch (err) {
-            error(err instanceof Error ? err.message : String(err));
-            process.exit(1);
-        }
-    });
-    // Parse and run
-    program.parse();
-} // end main()
-//# sourceMappingURL=codegraph.js.map