cgraphx 1.1.0

package/dist/bin/codegraph.js

@@ -0,0 +1,2014 @@
+#!/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);
+        }
+    });
+    /**
+     * cgraphx impact <symbol>
+     */
+    program
+        .command('impact <symbol>')
+        .description('Analyze what code is affected by changing a symbol')
+        .option('-p, --path <path>', 'Project path')
+        .option('-d, --depth <number>', 'Traversal depth', '2')
+        .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 ${projectPath}`);
+                process.exit(1);
+            }
+            const { default: CodeGraph } = await loadCodeGraph();
+            const cg = await CodeGraph.open(projectPath);
+            const depth = Math.min(Math.max(parseInt(options.depth || '2', 10), 1), 10);
+            const matches = cg.searchNodes(symbol, { limit: 50 });
+            if (matches.length === 0) {
+                info(`Symbol "${symbol}" not found`);
+                cg.destroy();
+                return;
+            }
+            // Merge impact subgraphs across all exact-matching symbols
+            const mergedNodes = new Map();
+            const seenEdges = new Set();
+            let edgeCount = 0;
+            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;
+                const impact = cg.getImpactRadius(match.node.id, depth);
+                for (const [id, n] of impact.nodes) {
+                    mergedNodes.set(id, { name: n.name, kind: n.kind, filePath: n.filePath, startLine: n.startLine });
+                }
+                for (const e of impact.edges) {
+                    const key = `${e.source}->${e.target}:${e.kind}`;
+                    if (!seenEdges.has(key)) {
+                        seenEdges.add(key);
+                        edgeCount++;
+                    }
+                }
+            }
+            // Fallback to top match if exact filter removed everything
+            if (mergedNodes.size === 0 && matches[0]) {
+                const impact = cg.getImpactRadius(matches[0].node.id, depth);
+                for (const [id, n] of impact.nodes) {
+                    mergedNodes.set(id, { name: n.name, kind: n.kind, filePath: n.filePath, startLine: n.startLine });
+                }
+                edgeCount = impact.edges.length;
+            }
+            if (options.json) {
+                console.log(JSON.stringify({
+                    symbol,
+                    depth,
+                    nodeCount: mergedNodes.size,
+                    edgeCount,
+                    affected: Array.from(mergedNodes.values()),
+                }, null, 2));
+            }
+            else if (mergedNodes.size === 0) {
+                info(`No affected symbols found for "${symbol}"`);
+            }
+            else {
+                console.log(chalk.bold(`\nImpact of changing "${symbol}" — ${mergedNodes.size} affected symbols:\n`));
+                // Group by file
+                const byFile = new Map();
+                for (const node of mergedNodes.values()) {
+                    const list = byFile.get(node.filePath) || [];
+                    list.push({ name: node.name, kind: node.kind, startLine: node.startLine });
+                    byFile.set(node.filePath, list);
+                }
+                for (const [file, nodes] of byFile) {
+                    console.log(chalk.cyan(file));
+                    for (const node of nodes) {
+                        const loc = node.startLine ? `:${node.startLine}` : '';
+                        console.log(`  ${chalk.dim(node.kind.padEnd(12))}${node.name}${chalk.dim(loc)}`);
+                    }
+                    console.log();
+                }
+            }
+            cg.destroy();
+        }
+        catch (err) {
+            error(`impact failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * cgraphx affected [files...]
+     *
+     * Find test files affected by the given source files.
+     * Traces dependency edges transitively to find test files that depend on changed code.
+     *
+     * Usage:
+     *   git diff --name-only | cgraphx affected --stdin
+     *   cgraphx affected src/lib/components/Editor.svelte src/routes/+page.svelte
+     */
+    program
+        .command('affected [files...]')
+        .description('Find test files affected by changed source files')
+        .option('-p, --path <path>', 'Project path')
+        .option('--stdin', 'Read file list from stdin (one per line)')
+        .option('-d, --depth <number>', 'Max dependency traversal depth', '5')
+        .option('-f, --filter <glob>', 'Custom glob filter for test files (e.g. "e2e/*.spec.ts")')
+        .option('-j, --json', 'Output as JSON')
+        .option('-q, --quiet', 'Only output file paths, no decoration')
+        .action(async (fileArgs, options) => {
+        const projectPath = resolveProjectPath(options.path);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`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