cgraphx 1.4.3 → 2.0.1

package/dist/bin/codegraph.js

@@ -1,1914 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * cgraphx CLI
- *
- * Command-line interface for cgraphx code intelligence.
- *
- * Usage:
- *   cgraphx                      Run interactive installer (when no args)
- *   cgraphx install              Run interactive installer
- *   cgraphx uninstall            Remove cgraphx from your agents
- *   cgraphx init [path]          Initialize cgraphx in a project
- *   cgraphx uninit [path]        Remove cgraphx from a project
- *   cgraphx index [path]         Index all files in the project
- *   cgraphx sync [path]          Sync changes since last index
- *   cgraphx status [path]        Show index status
- *   cgraphx query <search>       Search for symbols
- *   cgraphx files [options]      Show project file structure
- *   cgraphx context <task>       Build context for a task
- *   cgraphx callers <symbol>     Find what calls a function/method
- *   cgraphx callees <symbol>     Find what a function/method calls
- *   cgraphx impact <symbol>      Analyze what code is affected by changing a symbol
- *   cgraphx affected [files]     Find test files affected by changes
- *   cgraphx upgrade [version]    Update cgraphx to the latest release
- */
-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 worktree_1 = require("../sync/worktree");
-const shimmer_progress_1 = require("../ui/shimmer-progress");
-const glyphs_1 = require("../ui/glyphs");
-const node_version_check_1 = require("./node-version-check");
-const fatal_handler_1 = require("./fatal-handler");
-const wasm_runtime_flags_1 = require("../extraction/wasm-runtime-flags");
-const extraction_version_1 = require("../extraction/extraction-version");
-const telemetry_1 = require("../telemetry");
-const cli_1 = require("../markdown/cli");
-const cli_2 = require("../dbquery/cli");
-const cli_3 = require("../timeline/cli");
-const upgrade_1 = require("../upgrade");
-// 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 cgraphx 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 ${upgrade_1.NPM_PACKAGE}\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 cgraphx 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.
-// Node 25.x hard-exits (known V8 turboshaft Zone OOM, #81). Node 26+ is
-// unverified but not blocked — the launcher's --liftoff-only flag keeps
-// tree-sitter on the Liftoff baseline compiler, away from the turboshaft
-// path where the bug lives, so the same crash should not fire. We still
-// warn loudly so users know they're off the verified track.
-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.CGRAPHX_ALLOW_UNSAFE_NODE) {
-        process.exit(1);
-    }
-    // Override active — banner shown for visibility, continuing.
-}
-else if (nodeMajor >= 26) {
-    process.stderr.write((0, node_version_check_1.buildNodeUntestedBanner)(nodeVersion) + '\n');
-    // No exit — warning only.
-}
-// Enforce the supported Node floor. `engines` in package.json only *warns* on
-// install (unless engine-strict), so hard-block here to actually keep users off
-// unsupported versions. Mirrors the 25+ block above. See package.json `engines`.
-if (nodeMajor < node_version_check_1.MIN_NODE_MAJOR) {
-    process.stderr.write((0, node_version_check_1.buildNodeTooOldBanner)(nodeVersion) + '\n');
-    if (!process.env.CGRAPHX_ALLOW_UNSAFE_NODE) {
-        process.exit(1);
-    }
-    // Override active — banner shown for visibility, continuing.
-}
-// Re-exec with V8's `--liftoff-only` if it isn't already set, so tree-sitter's
-// large WASM grammars never hit the turboshaft Zone OOM (`Fatal process out of
-// memory: Zone`) on Node >= 22. No-op under the bundled launcher, which already
-// passes the flag. Must run before any grammar (in the parse worker, which
-// inherits this process's flags) is compiled. See ../extraction/wasm-runtime-flags.
-(0, wasm_runtime_flags_1.relaunchWithWasmRuntimeFlagsIfNeeded)(__filename);
-// Last-resort fatal handlers: log a bounded line and exit non-zero. A fault
-// that reaches here escaped every boundary, so the process is in an undefined
-// state — keeping it alive is what let the detached MCP daemon orphan and pin a
-// CPU core with no recovery (#799, #850). Installed before the command branch
-// so it also covers a synchronous throw during startup. See ./fatal-handler.
-(0, fatal_handler_1.installFatalHandlers)();
-// 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();
-}
-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'));
-    // Make the version trivial to reach. commander's `.version()` (below) wires up
-    // `--version` and `-V`; intercept the spellings it can't — lowercase `-v` and
-    // single-dash `-version` — before any parsing. (commander's version short flag
-    // is the capital `-V`, and its parser rejects a multi-character single-dash
-    // flag.) The bare `cgraphx version` subcommand is registered further down so
-    // the affordance also shows up in `cgraphx --help`.
-    const firstArg = process.argv[2];
-    if (firstArg === '-v' || firstArg === '-version') {
-        console.log(packageJson.version);
-        return;
-    }
-    // =============================================================================
-    // 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('cgraphx')
-        .description('Code intelligence and knowledge graph for any codebase')
-        .version(packageJson.version);
-    // Anonymous usage telemetry (see TELEMETRY.md): record the invoked subcommand
-    // NAME only — never arguments or paths. Counts buffer locally; network sends
-    // piggyback on commands that run long anyway (quick commands only append to
-    // the local buffer at exit, costing nothing).
-    // install/uninstall are absent on purpose: the installer flushes at its own
-    // end, AFTER its consent prompt — a flush here would fire the first-run
-    // notice before the user ever sees the toggle.
-    const TELEMETRY_FLUSH_COMMANDS = new Set(['init', 'uninit', 'index', 'sync', 'upgrade']);
-    program.hook('preAction', (_thisCommand, actionCommand) => {
-        try {
-            // The detached daemon re-invokes `serve --mcp` internally — not a user action.
-            if (process.env.CGRAPHX_DAEMON_INTERNAL)
-                return;
-            const name = actionCommand.name();
-            if (name === 'telemetry')
-                return; // managing telemetry is not usage
-            (0, telemetry_1.getTelemetry)().recordUsage('cli_command', name, true);
-            if (TELEMETRY_FLUSH_COMMANDS.has(name))
-                (0, telemetry_1.getTelemetry)().maybeFlush();
-        }
-        catch {
-            /* telemetry must never break the CLI */
-        }
-    });
-    // =============================================================================
-    // Helper Functions
-    // =============================================================================
-    /**
-     * Resolve project path from argument or current directory
-     * Walks up parent directories to find nearest initialized cgraphx project
-     * (must have .cgraphx/cgraphx.db, not just .cgraphx/lessons.db)
-     */
-    function resolveProjectPath(pathArg) {
-        const absolutePath = path.resolve(pathArg || process.cwd());
-        // If exact path is initialized (has cgraphx.db), use it
-        if ((0, directory_1.isInitialized)(absolutePath)) {
-            return absolutePath;
-        }
-        // Walk up to find nearest parent with cgraphx initialized
-        // Note: findNearestCodeGraphRoot finds any .cgraphx folder, but we need one with cgraphx.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 .cgraphx/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((0, directory_1.getCodeGraphDir)(projectPath), 'errors.log');
-            if (fs.existsSync(logPath)) {
-                fs.unlinkSync(logPath);
-            }
-        }
-    }
-    /**
-     * Write detailed error log to .cgraphx/errors.log
-     */
-    function writeErrorLog(projectPath, errors) {
-        const cgDir = (0, directory_1.getCodeGraphDir)(projectPath);
-        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 = [
-            `cgraphx 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');
-    }
-    /**
-     * Telemetry for a completed full index (see TELEMETRY.md). The bounded flush
-     * keeps init/index responsive (these commands just ran for seconds anyway)
-     * while delivering the event promptly.
-     */
-    async function recordIndexTelemetry(cg, result) {
-        (0, telemetry_1.recordIndexEvent)(cg, result);
-        await (0, telemetry_1.getTelemetry)().flushNow();
-    }
-    // =============================================================================
-    // Commands
-    // =============================================================================
-    /**
-     * cgraphx init [path]
-     */
-    program
-        .command('init [path]')
-        .description('Initialize cgraphx in a project directory and build the initial index')
-        .option('-i, --index', 'Deprecated: indexing now runs by default; flag accepted for backward compatibility')
-        .option('-f, --force', 'Initialize even if the path looks like your home directory or a filesystem root')
-        .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 cgraphx');
-        try {
-            // Refuse to index your home directory / a filesystem root — it pulls in
-            // caches, other projects, and your whole tree (a multi-GB index + watcher
-            // churn, and on pre-1.0 macOS a machine-crashing fd blowup, #845).
-            const unsafe = (0, directory_1.unsafeIndexRootReason)(projectPath);
-            if (unsafe && !options.force) {
-                clack.log.error(`Refusing to initialize in ${projectPath} — it looks like ${unsafe}.`);
-                clack.log.info('Run this inside a specific project directory, or pass --force if you really mean to index everything under it.');
-                clack.outro('');
-                process.exitCode = 1;
-                return;
-            }
-            if ((0, directory_1.isInitialized)(projectPath)) {
-                clack.log.warn(`Already initialized in ${projectPath}`);
-                clack.log.info('Use "cgraphx index" to re-index or "cgraphx sync" to update');
-                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 ${projectPath}`);
-            // Indexing runs by default now. The legacy -i/--index flag is still
-            // accepted (so existing muscle memory and scripts don't break) but is a
-            // no-op — initializing always builds the initial index.
-            let result;
-            if (options.verbose) {
-                result = await cg.indexAll({
-                    onProgress: createVerboseProgress(),
-                    verbose: true,
-                });
-            }
-            else {
-                process.stdout.write(`${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);
-            await recordIndexTelemetry(cg, result);
-            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);
-        }
-    });
-    /**
-     * cgraphx uninit [path]
-     */
-    program
-        .command('uninit [path]')
-        .description('Remove cgraphx from a project (deletes .cgraphx/ directory)')
-        .option('-f, --force', 'Skip confirmation prompt')
-        .action(async (pathArg, options) => {
-        const projectPath = resolveProjectPath(pathArg);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                warn(`cgraphx 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 cgraphx 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 cgraphx from ${projectPath}`);
-            // Churn signal — and flush now, since after an uninit there may be no
-            // "next run" to deliver it.
-            try {
-                (0, telemetry_1.getTelemetry)().recordLifecycle('uninstall', {});
-                await (0, telemetry_1.getTelemetry)().flushNow();
-            }
-            catch { /* non-fatal */ }
-        }
-        catch (err) {
-            error(`Failed to uninitialize: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx index [path]
-     */
-    program
-        .command('index [path]')
-        .description('Rebuild the full index from scratch (same result as a fresh init)')
-        .option('-f, --force', 'Index even if the path looks like your home directory or a filesystem root')
-        .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 {
-            // Don't (re)index your home directory / a filesystem root (#845). --force
-            // doubles as the override.
-            const unsafe = (0, directory_1.unsafeIndexRootReason)(projectPath);
-            if (unsafe && !options.force) {
-                error(`Refusing to index ${projectPath} — it looks like ${unsafe}. Pass --force to override.`);
-                process.exit(1);
-            }
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`cgraphx not initialized in ${projectPath}`);
-                info('Run "cgraphx init" first');
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            if (options.quiet) {
-                // Quiet mode: no UI, just run. `index` is a full re-index, so clear the
-                // existing graph and rebuild from scratch (see the note below — #874).
-                cg.clear();
-                const result = await cg.indexAll();
-                if (!result.success)
-                    process.exit(1);
-                cg.destroy();
-                return;
-            }
-            const clack = await importESM('@clack/prompts');
-            clack.intro('Indexing project');
-            // `index` is a FULL re-index: clear the existing graph and rebuild it from
-            // scratch so the result is identical to a fresh `init`. Without the clear,
-            // indexAll() skips every unchanged file by its content hash and reports
-            // "0 nodes, 0 edges" against the already-populated graph — which reads as
-            // "index wiped my index" (#874). For fast incremental updates use `sync`.
-            cg.clear();
-            let result;
-            if (options.verbose) {
-                result = await cg.indexAll({
-                    onProgress: createVerboseProgress(),
-                    verbose: true,
-                });
-            }
-            else {
-                process.stdout.write(`${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);
-            await recordIndexTelemetry(cg, result);
-            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);
-        }
-    });
-    /**
-     * cgraphx 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(`cgraphx not initialized in ${projectPath}`);
-                }
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            if (options.quiet) {
-                await cg.sync();
-                cg.destroy();
-                return;
-            }
-            const clack = await importESM('@clack/prompts');
-            clack.intro('Syncing cgraphx');
-            process.stdout.write(`${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);
-        }
-    });
-    /**
-     * cgraphx 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);
-        // The directory the user actually ran from, before walking up to the index
-        // root. Used to detect when the resolved index lives in a different git
-        // working tree (e.g. a nested worktree borrowing the main checkout's index).
-        const startPath = path.resolve(pathArg || process.cwd());
-        const worktreeMismatch = (0, worktree_1.detectWorktreeIndexMismatch)(startPath, projectPath);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                if (options.json) {
-                    console.log(JSON.stringify({
-                        initialized: false,
-                        version: packageJson.version,
-                        projectPath,
-                        indexPath: (0, directory_1.getCodeGraphDir)(projectPath),
-                        lastIndexed: null,
-                    }));
-                    return;
-                }
-                console.log(chalk.bold('\ncgraphx Status\n'));
-                info(`Project: ${projectPath}`);
-                warn('Not initialized');
-                info('Run "cgraphx 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();
-            const journalMode = cg.getJournalMode();
-            const buildInfo = cg.getIndexBuildInfo();
-            const reindexRecommended = cg.isIndexStale();
-            // JSON output mode
-            if (options.json) {
-                const lastIndexedMs = cg.getLastIndexedAt();
-                console.log(JSON.stringify({
-                    initialized: true,
-                    version: packageJson.version,
-                    projectPath,
-                    indexPath: (0, directory_1.getCodeGraphDir)(projectPath),
-                    lastIndexed: lastIndexedMs != null ? new Date(lastIndexedMs).toISOString() : null,
-                    fileCount: stats.fileCount,
-                    nodeCount: stats.nodeCount,
-                    edgeCount: stats.edgeCount,
-                    dbSizeBytes: stats.dbSizeBytes,
-                    backend,
-                    journalMode,
-                    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,
-                    },
-                    worktreeMismatch: worktreeMismatch
-                        ? { worktreeRoot: worktreeMismatch.worktreeRoot, indexRoot: worktreeMismatch.indexRoot }
-                        : null,
-                    index: {
-                        builtWithVersion: buildInfo.version,
-                        builtWithExtractionVersion: buildInfo.extractionVersion,
-                        currentExtractionVersion: extraction_version_1.EXTRACTION_VERSION,
-                        reindexRecommended,
-                    },
-                }));
-                cg.destroy();
-                return;
-            }
-            console.log(chalk.bold('\ncgraphx Status\n'));
-            // Project info
-            console.log(chalk.cyan('Project:'), projectPath);
-            if (worktreeMismatch) {
-                warn((0, worktree_1.worktreeMismatchWarning)(worktreeMismatch));
-            }
-            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 (node:sqlite — Node's built-in real
-            // SQLite, full WAL + FTS5, no native build).
-            const backendLabel = chalk.green(`node:sqlite ${(0, glyphs_1.getGlyphs)().dash} built-in (full WAL)`);
-            console.log(`  Backend:   ${backendLabel}`);
-            // Effective journal mode: 'wal' means concurrent reads never block on a
-            // writer; anything else means they can ("database is locked"). node:sqlite
-            // supports WAL everywhere, so a non-wal mode means the filesystem can't
-            // (network mounts, WSL2 /mnt). See issue #238.
-            const journalLabel = journalMode === 'wal'
-                ? chalk.green('wal')
-                : chalk.yellow(`${journalMode || 'unknown'} ${(0, glyphs_1.getGlyphs)().dash} WAL inactive; reads can block on writes`);
-            console.log(`  Journal:   ${journalLabel}`);
-            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:   ${changes.removed.length} files`);
-                }
-                info('Run "cgraphx sync" to update the index');
-            }
-            else {
-                success('Index is up to date');
-            }
-            console.log();
-            // Re-index hint: the index was built by an older engine than the one now
-            // running, so a rebuild would add data a migration can't backfill.
-            if (reindexRecommended) {
-                const builtWith = buildInfo.version ? `v${buildInfo.version.replace(/^v/, '')}` : 'an earlier version';
-                warn(`Index was built by ${builtWith}; re-index to pick up this engine's improvements.`);
-                info('Run "cgraphx index" (full rebuild) or "cgraphx sync"');
-                console.log();
-            }
-            cg.destroy();
-        }
-        catch (err) {
-            error(`Failed to get status: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx 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(`cgraphx not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const limit = parseInt(options.limit || '10', 10);
-            const rawResults = cg.searchNodes(search, {
-                limit,
-                kinds: options.kind ? [options.kind] : undefined,
-            });
-            // Mirror the MCP search down-rank so the CLI also surfaces the
-            // hand-written implementation before protobuf/gRPC scaffolding
-            // when both share a name. See extraction/generated-detection.ts.
-            const { isGeneratedFile } = await Promise.resolve().then(() => __importStar(require('../extraction/generated-detection')));
-            const results = [...rawResults].sort((a, b) => {
-                const aGen = isGeneratedFile(a.node.filePath) ? 1 : 0;
-                const bGen = isGeneratedFile(b.node.filePath) ? 1 : 0;
-                return aGen - bGen;
-            });
-            if (options.json) {
-                console.log(JSON.stringify(results, null, 2));
-            }
-            else {
-                if (results.length === 0) {
-                    info(`No results found for "${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);
-        }
-    });
-    /**
-     * cgraphx explore <query...>
-     *
-     * The CLI face of the MCP codegraph_explore tool — same handler, same
-     * output (source of the relevant symbols grouped by file + the call path
-     * among them). Exists so agents WITHOUT the MCP tools — Task-tool
-     * subagents (which don't inherit MCP tools, #704) and non-MCP harnesses —
-     * can reach the graph through a plain shell command.
-     */
-    program
-        .command('explore <query...>')
-        .description('Explore an area: relevant symbols\' source + call paths in one shot (same output as the codegraph_explore MCP tool)')
-        .option('-p, --path <path>', 'Project path')
-        .option('--max-files <number>', 'Maximum number of files to include source from')
-        .action(async (queryParts, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`cgraphx isn't available here — no .cgraphx/ index exists in ${projectPath}. If you are an AI agent: continue with your usual tools; indexing is the user's decision, do not run it yourself. (The project owner can enable cgraphx with 'cgraphx init'.)`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const { ToolHandler } = await Promise.resolve().then(() => __importStar(require('../mcp/tools')));
-            const handler = new ToolHandler(cg);
-            const args = { query: queryParts.join(' ') };
-            if (options.maxFiles)
-                args.maxFiles = parseInt(options.maxFiles, 10);
-            const result = await handler.execute('codegraph_explore', args);
-            console.log(result.content[0]?.text ?? '');
-            cg.destroy();
-            if (result.isError)
-                process.exit(1);
-        }
-        catch (err) {
-            error(`Explore failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx prompt-hook  (hidden)
-     *
-     * A Claude Code `UserPromptSubmit` hook entry point. Reads `{prompt, cwd}` JSON
-     * on stdin; for a structural/flow/impact prompt it runs `codegraph_explore` on
-     * the indexed project and prints the result to stdout, which Claude injects into
-     * the agent's context — so the agent's reflex grep/read has nothing left to find
-     * and reliably uses cgraphx (the adoption problem). Installed by the installer
-     * into Claude's settings.json (opt-in, default-yes).
-     *
-     * LOAD-BEARING: this must NEVER break the user's prompt. Every failure path —
-     * kill-switch, non-structural prompt, no index, engine error — exits 0 with no
-     * output. The only effect is additive context when it can confidently provide it.
-     */
-    program
-        .command('prompt-hook', { hidden: true })
-        .description('Claude UserPromptSubmit hook: inject cgraphx context for structural prompts (reads {prompt,cwd} JSON on stdin)')
-        .action(async () => {
-        try {
-            // Kill-switch: lets a user disable the nudge without uninstalling /
-            // editing settings.json (CI, low-power machines, personal preference).
-            if (process.env.CGRAPHX_NO_PROMPT_HOOK === '1' || process.env.CGRAPHX_PROMPT_HOOK === '0')
-                return;
-            if (process.stdin.isTTY)
-                return; // invoked by hand, no piped payload
-            const raw = await new Promise((resolve) => {
-                let data = '';
-                process.stdin.setEncoding('utf8');
-                process.stdin.on('data', (c) => { data += c; });
-                process.stdin.on('end', () => resolve(data));
-                process.stdin.on('error', () => resolve(data));
-            });
-            let input = {};
-            try {
-                input = JSON.parse(raw);
-            }
-            catch {
-                return;
-            }
-            const prompt = String(input.prompt || '');
-            // Gate: only structural / flow / impact / where-how prompts get context.
-            // A cheap regex keeps every other prompt ("fix this typo") a zero-cost
-            // no-op so we never add latency where there's no structural answer to give.
-            const STRUCTURAL = /\b(how|where|trace|flow|path|reach(?:es|ed)?|call(?:s|ed|er|ers|ee)?|depend|impact|affect|wired?|connect|implement|architect|structure|breaks?|what calls|why does)\b/i;
-            if (!prompt || !STRUCTURAL.test(prompt))
-                return;
-            // Decide what to inject, shaped by WHERE the index(es) are: the nearest
-            // indexed ancestor of cwd, or — when cwd is an un-indexed workspace root
-            // whose indexed project(s) live in sub-dirs (the monorepo case, #964) —
-            // the sub-project the prompt points at, plus a `projectPath` nudge for any
-            // others. Without the down-scan the hook injected nothing at a monorepo
-            // root (it only walked up), so the validated adoption lever never fired
-            // exactly where the agent most needs it.
-            const plan = (0, directory_1.planFrontload)(String(input.cwd || process.cwd()), prompt);
-            if (!plan.exploreRoot && plan.nudgeProjects.length === 0)
-                return; // nothing reachable — the agent's normal tools apply
-            // A "pass projectPath" line for indexed sub-projects we did NOT front-load.
-            // Follow-up codegraph_explore calls against a sub-project (cwd isn't its
-            // index root) need an explicit projectPath, so spell it out.
-            const nudge = (projects, lead) => `${lead}\n${projects.map((p) => `  - projectPath: "${p}"`).join('\n')}\n`;
-            if (plan.exploreRoot) {
-                const { default: CodeGraph } = await loadCodeGraph();
-                const cg = await CodeGraph.open(plan.exploreRoot);
-                try {
-                    const { ToolHandler } = await Promise.resolve().then(() => __importStar(require('../mcp/tools')));
-                    const handler = new ToolHandler(cg);
-                    const result = await handler.execute('codegraph_explore', { query: prompt });
-                    const text = result.content[0]?.text ?? '';
-                    if (!result.isError && text.trim()) {
-                        // Cap the injection so a large-repo explore can't flood the prompt.
-                        const MAX = 16000;
-                        const body = text.length > MAX ? `${text.slice(0, MAX)}\n…(truncated; call codegraph_explore for the rest)` : text;
-                        // For a front-loaded SUB-project, a follow-up explore needs its path.
-                        const more = plan.viaSubScan
-                            ? `call codegraph_explore with projectPath: "${plan.exploreRoot}" for more`
-                            : 'call codegraph_explore for more';
-                        const others = plan.nudgeProjects.length
-                            ? `\n${nudge(plan.nudgeProjects, 'Other indexed projects in this workspace — pass projectPath to query them:')}`
-                            : '';
-                        process.stdout.write(`<codegraph_context note="Structural context from cgraphx for this prompt — treat returned source as already read; ${more}.">\n${body}${others}\n</codegraph_context>\n`);
-                    }
-                }
-                finally {
-                    cg.destroy();
-                }
-            }
-            else {
-                // Several indexed sub-projects, none a clear match — don't guess; tell
-                // the agent they exist and how to query one.
-                process.stdout.write(`<codegraph_context note="cgraphx is available for this workspace's indexed sub-projects — query one by passing projectPath to codegraph_explore.">\n` +
-                    nudge(plan.nudgeProjects, "This workspace's cgraphx indexes live in sub-projects. To use cgraphx, call codegraph_explore with the projectPath of the relevant one:") +
-                    `</codegraph_context>\n`);
-            }
-        }
-        catch {
-            // Degradable by contract: never surface an error to the prompt pipeline.
-        }
-    });
-    /**
-     * cgraphx node <name>
-     *
-     * The CLI face of the MCP codegraph_node tool: one symbol's source +
-     * caller/callee trail, or a whole file with line numbers + dependents
-     * (Read-parity). Same subagent/non-MCP rationale as `explore`.
-     */
-    program
-        .command('node <name>')
-        .description('One symbol\'s source + caller/callee trail, or read a file with line numbers + dependents (same output as the codegraph_node MCP tool)')
-        .option('-p, --path <path>', 'Project path')
-        .option('-f, --file <file>', 'Treat as file mode (or disambiguate a symbol to this file)')
-        .option('--offset <number>', 'File mode: 1-based start line')
-        .option('--limit <number>', 'File mode: maximum lines')
-        .option('--symbols-only', 'File mode: just the symbol map + dependents')
-        .action(async (name, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`cgraphx isn't available here — no .cgraphx/ index exists in ${projectPath}. If you are an AI agent: continue with your usual tools; indexing is the user's decision, do not run it yourself. (The project owner can enable cgraphx with 'cgraphx init'.)`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const { ToolHandler } = await Promise.resolve().then(() => __importStar(require('../mcp/tools')));
-            const handler = new ToolHandler(cg);
-            // A name with a path separator is a file read; otherwise a symbol
-            // (use --file for basename-only file reads or to pin an overload).
-            // Both separators: Windows users type src\auth\session.ts. Symbols
-            // never contain either ('/' isn't an identifier char anywhere we
-            // index; C++ scope is '::', JS members '.').
-            const args = {};
-            if (options.file) {
-                args.file = options.file;
-                if (name && name !== options.file)
-                    args.symbol = name;
-            }
-            else if (name.includes('/') || name.includes('\\')) {
-                args.file = name.replace(/\\/g, '/');
-            }
-            else {
-                args.symbol = name;
-                args.includeCode = true;
-            }
-            if (options.offset)
-                args.offset = parseInt(options.offset, 10);
-            if (options.limit)
-                args.limit = parseInt(options.limit, 10);
-            if (options.symbolsOnly)
-                args.symbolsOnly = true;
-            const result = await handler.execute('codegraph_node', args);
-            console.log(result.content[0]?.text ?? '');
-            cg.destroy();
-            if (result.isError)
-                process.exit(1);
-        }
-        catch (err) {
-            error(`Node lookup failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx 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(`cgraphx not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            let files = cg.getFiles();
-            if (files.length === 0) {
-                info('No files indexed. Run "cgraphx index" first.');
-                cg.destroy();
-                return;
-            }
-            // Filter by path prefix
-            if (options.filter) {
-                const filter = options.filter;
-                files = files.filter(f => f.path.startsWith(filter) || f.path.startsWith('./' + filter));
-            }
-            // Filter by glob pattern
-            if (options.pattern) {
-                const regex = globToRegex(options.pattern);
-                files = files.filter(f => regex.test(f.path));
-            }
-            if (files.length === 0) {
-                info('No files found matching the criteria.');
-                cg.destroy();
-                return;
-            }
-            // JSON output
-            if (options.json) {
-                const output = files.map(f => ({
-                    path: f.path,
-                    language: f.language,
-                    nodeCount: f.nodeCount,
-                    size: f.size,
-                }));
-                console.log(JSON.stringify(output, null, 2));
-                cg.destroy();
-                return;
-            }
-            const includeMetadata = options.metadata !== false;
-            const format = options.format || 'tree';
-            const maxDepth = options.maxDepth ? parseInt(options.maxDepth, 10) : undefined;
-            // Format output
-            switch (format) {
-                case 'flat':
-                    console.log(chalk.bold(`\nFiles (${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: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * Normalize a user-supplied file path to the project-relative, forward-slash
-     * form cgraphx stores in the index. Accepts an absolute path, a `./`-prefixed
-     * path, or Windows back-slashes; an empty string when the input is blank. Used
-     * by `cgraphx affected` so `./src/x.ts`, `/abs/repo/src/x.ts`, and
-     * `src/x.ts` all match the same indexed file. (#825)
-     */
-    function normalizeIndexPath(filePath, projectPath) {
-        let f = filePath.trim();
-        if (!f)
-            return '';
-        if (path.isAbsolute(f))
-            f = path.relative(projectPath, f);
-        // Collapse `.`/`..` segments, then force forward slashes and drop a leading
-        // `./` (path.normalize already strips it on POSIX; explicit for Windows).
-        f = path.normalize(f).replace(/\\/g, '/').replace(/^\.\//, '');
-        return f;
-    }
-    /**
-     * Convert glob pattern to regex
-     */
-    function globToRegex(pattern) {
-        const escaped = pattern
-            .replace(/[.+^${}()|[\]\\]/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);
-    }
-    /**
-     * cgraphx daemon — interactive manager for the background daemons. Arrow keys
-     * to pick one (the current project's daemon floats to the top, auto-selected),
-     * enter to stop it. Falls back to a plain list when output isn't a TTY.
-     */
-    program
-        .command('daemon')
-        .aliases(['daemons'])
-        .description('Manage running cgraphx background daemons — pick one and press enter to stop it')
-        .action(async () => {
-        const { listDaemons, stopDaemonAt, stopAllDaemons } = await Promise.resolve().then(() => __importStar(require('../mcp/daemon-registry')));
-        const { runDaemonPicker } = await Promise.resolve().then(() => __importStar(require('../mcp/daemon-manager')));
-        const daemons = listDaemons();
-        if (daemons.length === 0) {
-            info('No cgraphx daemons running.');
-            return;
-        }
-        // No TTY (piped / CI / non-interactive) — can't do arrow-key selection, so
-        // just print what's running instead of crashing on a prompt with no input.
-        if (!process.stdout.isTTY || !process.stdin.isTTY) {
-            for (const d of daemons) {
-                console.log(`pid ${d.pid}  v${d.version}  up ${formatDuration(Date.now() - d.startedAt)}  ${d.root}`);
-            }
-            return;
-        }
-        // The current project's daemon floats to the top and is pre-selected.
-        let cwdRoot = null;
-        const found = (0, directory_1.findNearestCodeGraphRoot)(process.cwd());
-        if (found) {
-            try {
-                cwdRoot = fs.realpathSync(found);
-            }
-            catch {
-                cwdRoot = found;
-            }
-        }
-        const clack = await importESM('@clack/prompts');
-        clack.intro('cgraphx daemons');
-        await runDaemonPicker({
-            list: listDaemons,
-            stop: stopDaemonAt,
-            stopAll: stopAllDaemons,
-            cwdRoot,
-            now: () => Date.now(),
-            select: (opts) => clack.select(opts),
-            isCancel: (v) => clack.isCancel(v),
-            note: (m) => clack.log.success(m),
-            done: (m) => clack.outro(m),
-        });
-    });
-    /**
-     * cgraphx serve
-     */
-    program
-        // Hidden from `--help`: this is the stdio entry point an AI agent launches
-        // for itself (the installer wires `args: ['serve','--mcp']` into every
-        // agent's MCP config), not a command a human runs. It still works when
-        // invoked — hiding only removes it from the listing. See the interactive-TTY
-        // guard below, which explains this to anyone who runs it by hand.
-        .command('serve', { hidden: true })
-        .description('Start cgraphx 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.CGRAPHX_NO_WATCH = '1';
-        }
-        try {
-            if (options.mcp) {
-                // `serve --mcp` is the stdio MCP server an AI agent launches for itself,
-                // not a command to run by hand. A human in a terminal would otherwise
-                // see it hang waiting for JSON-RPC on stdin, which reads as broken. If
-                // stdin is an interactive TTY, explain instead of hanging. The agent's
-                // pipe and the detached daemon both have a non-TTY stdin, so this only
-                // ever fires for a person who typed it.
-                if (process.stdin.isTTY && !process.env.CGRAPHX_DAEMON_INTERNAL) {
-                    console.error(chalk.bold('\ncgraphx MCP server\n'));
-                    console.error("This is the MCP server your AI agent (Claude Code, Cursor, Codex, opencode, …)");
-                    console.error("starts automatically — you don't run it yourself.");
-                    console.error(`\nIt's already wired up by ${chalk.cyan('cgraphx install')}. To check on things:`);
-                    console.error(`  ${chalk.cyan('cgraphx status')}   ${chalk.dim('— is this project indexed and healthy?')}`);
-                    console.error(`  ${chalk.cyan('cgraphx daemon')}   ${chalk.dim('— list or stop background MCP servers')}`);
-                    console.error(chalk.dim('\n(Running it directly only does something when an MCP client drives it over stdin.)'));
-                    return;
-                }
-                // 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('\ncgraphx 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": {
-    "cgraphx": {
-      "command": "cgraphx",
-      "args": ["serve", "--mcp"]
-    }
-  }
-}
-`));
-                console.error('Available tools:');
-                console.error(chalk.cyan('  codegraph_explore') + '   - Primary: source of the relevant symbols for any question');
-                console.error(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
-                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);
-        }
-    });
-    /**
-     * cgraphx 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(`cgraphx not initialized in ${projectPath}`);
-                return;
-            }
-            const lockPath = path.join((0, directory_1.getCodeGraphDir)(projectPath), 'cgraphx.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);
-        }
-    });
-    /**
-     * cgraphx callers <symbol>
-     *
-     * CLI parity with the MCP graph tools (codegraph_callers/callees/impact) so the
-     * traversal queries work in scripts, CI, and git hooks without a running MCP
-     * server.
-     */
-    program
-        .command('callers <symbol>')
-        .description('Find all functions/methods that call a specific symbol')
-        .option('-p, --path <path>', 'Project path')
-        .option('-l, --limit <number>', 'Maximum results', '20')
-        .option('-j, --json', 'Output as JSON')
-        .action(async (symbol, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`cgraphx not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const limit = parseInt(options.limit || '20', 10);
-            const matches = cg.searchNodes(symbol, { limit: 50 });
-            if (matches.length === 0) {
-                info(`Symbol "${symbol}" not found`);
-                cg.destroy();
-                return;
-            }
-            const seen = new Set();
-            const allCallers = [];
-            for (const match of matches) {
-                const exactMatch = match.node.name === symbol || match.node.name.endsWith(`.${symbol}`) || match.node.name.endsWith(`::${symbol}`);
-                if (!exactMatch && matches.length > 1)
-                    continue;
-                for (const c of cg.getCallers(match.node.id)) {
-                    if (!seen.has(c.node.id)) {
-                        seen.add(c.node.id);
-                        allCallers.push({ name: c.node.name, kind: c.node.kind, filePath: c.node.filePath, startLine: c.node.startLine });
-                    }
-                }
-            }
-            // Fallback: if exact filter removed everything, use the top match
-            if (allCallers.length === 0 && matches[0]) {
-                for (const c of cg.getCallers(matches[0].node.id)) {
-                    if (!seen.has(c.node.id)) {
-                        seen.add(c.node.id);
-                        allCallers.push({ name: c.node.name, kind: c.node.kind, filePath: c.node.filePath, startLine: c.node.startLine });
-                    }
-                }
-            }
-            const limited = allCallers.slice(0, limit);
-            if (options.json) {
-                console.log(JSON.stringify({ symbol, callers: limited }, null, 2));
-            }
-            else if (limited.length === 0) {
-                info(`No callers found for "${symbol}"`);
-            }
-            else {
-                console.log(chalk.bold(`\nCallers of "${symbol}" (${limited.length}):\n`));
-                for (const node of limited) {
-                    const loc = node.startLine ? `:${node.startLine}` : '';
-                    console.log(chalk.cyan(node.kind.padEnd(12)) +
-                        chalk.white(node.name));
-                    console.log(chalk.dim(`  ${node.filePath}${loc}`));
-                    console.log();
-                }
-            }
-            cg.destroy();
-        }
-        catch (err) {
-            error(`callers failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx callees <symbol>
-     */
-    program
-        .command('callees <symbol>')
-        .description('Find all functions/methods that a specific symbol calls')
-        .option('-p, --path <path>', 'Project path')
-        .option('-l, --limit <number>', 'Maximum results', '20')
-        .option('-j, --json', 'Output as JSON')
-        .action(async (symbol, options) => {
-        const projectPath = resolveProjectPath(options.path);
-        try {
-            if (!(0, directory_1.isInitialized)(projectPath)) {
-                error(`cgraphx not initialized in ${projectPath}`);
-                process.exit(1);
-            }
-            const { default: CodeGraph } = await loadCodeGraph();
-            const cg = await CodeGraph.open(projectPath);
-            const limit = parseInt(options.limit || '20', 10);
-            const matches = cg.searchNodes(symbol, { limit: 50 });
-            if (matches.length === 0) {
-                info(`Symbol "${symbol}" not found`);
-                cg.destroy();
-                return;
-            }
-            const seen = new Set();
-            const allCallees = [];
-            for (const match of matches) {
-                const exactMatch = match.node.name === symbol || match.node.name.endsWith(`.${symbol}`) || match.node.name.endsWith(`::${symbol}`);
-                if (!exactMatch && matches.length > 1)
-                    continue;
-                for (const c of cg.getCallees(match.node.id)) {
-                    if (!seen.has(c.node.id)) {
-                        seen.add(c.node.id);
-                        allCallees.push({ name: c.node.name, kind: c.node.kind, filePath: c.node.filePath, startLine: c.node.startLine });
-                    }
-                }
-            }
-            if (allCallees.length === 0 && matches[0]) {
-                for (const c of cg.getCallees(matches[0].node.id)) {
-                    if (!seen.has(c.node.id)) {
-                        seen.add(c.node.id);
-                        allCallees.push({ name: c.node.name, kind: c.node.kind, filePath: c.node.filePath, startLine: c.node.startLine });
-                    }
-                }
-            }
-            const limited = allCallees.slice(0, limit);
-            if (options.json) {
-                console.log(JSON.stringify({ symbol, callees: limited }, null, 2));
-            }
-            else if (limited.length === 0) {
-                info(`No callees found for "${symbol}"`);
-            }
-            else {
-                console.log(chalk.bold(`\nCallees of "${symbol}" (${limited.length}):\n`));
-                for (const node of limited) {
-                    const loc = node.startLine ? `:${node.startLine}` : '';
-                    console.log(chalk.cyan(node.kind.padEnd(12)) +
-                        chalk.white(node.name));
-                    console.log(chalk.dim(`  ${node.filePath}${loc}`));
-                    console.log();
-                }
-            }
-            cg.destroy();
-        }
-        catch (err) {
-            error(`callees failed: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    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(`cgraphx 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);
-            }
-            // Normalize inputs to the project-relative, forward-slash form the index
-            // stores. Without this, `affected ./src/x.ts`, an absolute path (what a
-            // wrapping script often passes), or a Windows back-slash path silently
-            // matches nothing and reports 0 affected tests. (#825)
-            changedFiles = changedFiles
-                .map((f) => normalizeIndexPath(f, projectPath))
-                .filter(Boolean);
-            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: ${err instanceof Error ? err.message : String(err)}`);
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx install
-     */
-    program
-        .command('install')
-        .description('Install cgraphx MCP server into one or more agents (Claude Code, Cursor, Codex CLI, opencode, Hermes Agent)')
-        .option('-t, --target <ids>', 'Target agent(s): comma-separated ids, or "auto"|"all"|"none". Default: prompt')
-        .option('-l, --location <where>', 'Install location: "global" or "local". Default: prompt')
-        .option('-y, --yes', 'Non-interactive: defaults to --location=global --target=auto, auto-allow on')
-        .option('--no-permissions', 'Skip writing the auto-allow permissions list (Claude Code only)')
-        .option('--print-config <id>', 'Print MCP config snippet for the named agent and exit (no file writes)')
-        .action(async (opts) => {
-        if (opts.printConfig) {
-            const { getTarget, listTargetIds } = await Promise.resolve().then(() => __importStar(require('../installer/targets/registry')));
-            const target = getTarget(opts.printConfig);
-            if (!target) {
-                const known = listTargetIds().join(', ');
-                error(`Unknown target "${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);
-        }
-    });
-    /**
-     * cgraphx uninstall
-     *
-     * Inverse of `install`. Removes the codegraph MCP server entry,
-     * instructions block, and permissions from every agent (or a
-     * `--target` subset). Prompts global-vs-local when not given. Does NOT
-     * delete the `.cgraphx/` index — that's `cgraphx uninit`.
-     */
-    program
-        .command('uninstall')
-        .description('Remove cgraphx from your agents (Claude Code, Cursor, Codex CLI, opencode, Hermes Agent)')
-        .option('-t, --target <ids>', 'Target agent(s): comma-separated ids, or "all". Default: all')
-        .option('-l, --location <where>', 'Uninstall location: "global" or "local". Default: prompt')
-        .option('-y, --yes', 'Non-interactive: defaults to --location=global --target=all')
-        .action(async (opts) => {
-        const { runUninstaller } = 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 {
-            await runUninstaller({
-                target: opts.target,
-                location: opts.location,
-                yes: opts.yes,
-            });
-        }
-        catch (err) {
-            error(err instanceof Error ? err.message : String(err));
-            process.exit(1);
-        }
-    });
-    /**
-     * cgraphx telemetry [on|off|status]
-     */
-    program
-        .command('telemetry [action]')
-        .description('Show or change anonymous usage telemetry (status, on, off)')
-        .action((action) => {
-        const t = (0, telemetry_1.getTelemetry)();
-        if (action === 'on' || action === 'off') {
-            t.setEnabled(action === 'on', 'cli');
-            if (action === 'on') {
-                success('Telemetry enabled — anonymous usage stats only (no code, paths, or names).');
-            }
-            else {
-                success('Telemetry disabled. Buffered, unsent data was deleted.');
-            }
-            const effective = t.getStatus();
-            if (effective.decidedBy === 'DO_NOT_TRACK' || effective.decidedBy === 'CGRAPHX_TELEMETRY') {
-                warn(`The ${effective.decidedBy} environment variable overrides this choice — ` +
-                    `effective state right now: ${effective.enabled ? 'enabled' : 'disabled'}.`);
-            }
-            return;
-        }
-        if (action !== undefined && action !== 'status') {
-            error(`Unknown action: ${action} (expected status, on, or off)`);
-            process.exit(1);
-        }
-        const s = t.getStatus();
-        const decidedBy = {
-            DO_NOT_TRACK: 'DO_NOT_TRACK environment variable',
-            CGRAPHX_TELEMETRY: 'CGRAPHX_TELEMETRY environment variable',
-            config: 'your saved choice',
-            default: 'default',
-        };
-        console.log(`\nTelemetry: ${s.enabled ? chalk.green('enabled') : chalk.yellow('disabled')} ${chalk.dim(`(${decidedBy[s.decidedBy]})`)}`);
-        console.log(`Machine ID: ${s.machineId ?? chalk.dim('(random UUID, created on first use)')}`);
-        console.log(`Config:     ${s.configPath}`);
-        console.log(chalk.dim(`\nExactly what is collected (and never collected): ${telemetry_1.TELEMETRY_DOCS}\n`));
-    });
-    /**
-     * cgraphx upgrade [version]
-     *
-     * Self-update, however cgraphx was installed (bundle via install.sh/.ps1,
-     * npm-global, npx, or a source checkout). See ../upgrade for the detection and
-     * per-method upgrade logic.
-     */
-    program
-        .command('upgrade [version]')
-        .description('Update cgraphx to the latest release (or a specific version)')
-        .option('--check', 'Check whether an update is available without installing')
-        .option('-f, --force', 'Reinstall even if already on the target version')
-        .action(async (versionArg, options) => {
-        const up = await Promise.resolve().then(() => __importStar(require('../upgrade')));
-        const method = up.detectInstallMethod({
-            filename: __filename,
-            platform: process.platform,
-            cwd: process.cwd(),
-        });
-        const pin = versionArg || process.env.CGRAPHX_VERSION || undefined;
-        const code = await up.runUpgrade({ version: pin, check: options.check, force: options.force }, {
-            currentVersion: packageJson.version,
-            method,
-            resolveLatest: () => up.resolveLatestVersion(),
-            run: up.defaultRun,
-            hasCommand: up.hasCommand,
-            log: (m) => console.log(m),
-            warn: (m) => warn(m),
-            error: (m) => error(m),
-            platform: process.platform,
-        });
-        process.exit(code);
-    });
-    /**
-     * cgraphx version
-     *
-     * The bare-noun form of `--version`. commander already provides `--version`
-     * and `-V`, and the `-v` / `-version` spellings are intercepted before parse
-     * (see top of main). This subcommand makes `cgraphx version` work and lists
-     * the version affordance in `cgraphx --help`.
-     */
-    program
-        .command('version')
-        .description('Print the installed cgraphx version (also: -v, --version)')
-        .action(() => {
-        console.log(packageJson.version);
-    });
-    // Markdown knowledge base subsystem (independent of the code graph).
-    // Registration is a single function call so the docs command group stays
-    // isolated in src/markdown/cli.ts — see docs/features/2026-06-26-docs-knowledge-base/.
-    (0, cli_1.registerDocsCommands)(program);
-    // db-query subsystem — isolated in src/dbquery/cli.ts.
-    (0, cli_2.registerDbCommands)(program);
-    // timeline subsystem — isolated in src/timeline/cli.ts.
-    (0, cli_3.registerTimelineCommands)(program);
-    // Parse and run
-    program.parse();
-} // end main()
-//# sourceMappingURL=codegraph.js.map