@ltm-alpha/alpha-cs 1.6.0

package/dist/bin/ltm-alpha-cs.js

@@ -0,0 +1,2643 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Alpha Code Sense CLI (deprecated alias)
+ *
+ * Command-line interface for Alpha Code Sense code intelligence.
+ *
+ * Usage:
+ *   codegraph                    Run interactive installer (when no args)
+ *   codegraph install            Run interactive installer
+ *   ltm-alpha-cs uninstall          Remove Alpha Code Sense from your agents
+ *   codegraph init [path]        Initialize Alpha Code Sense in a project
+ *   codegraph uninit [path]      Remove Alpha Code Sense from a project
+ *   codegraph index [path]       Index all files in the project
+ *   codegraph sync [path]        Sync changes since last index
+ *   ltm-alpha-cs status [path]      Show index status
+ *   codegraph query <search>     Search for symbols
+ *   codegraph files [options]    Show project file structure
+ *   codegraph context <task>     Build context for a task
+ *   codegraph callers <symbol>   Find what calls a function/method
+ *   codegraph callees <symbol>   Find what a function/method calls
+ *   codegraph impact <symbol>    Analyze what code is affected by changing a symbol
+ *   codegraph affected [files]   Find test files affected by changes
+ *   codegraph ui [path]          Open the browser viewer for an indexed project (alias: web)
+ *   ltm-alpha-cs upgrade [version]  Update Alpha Code Sense 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 });
+// FIRST import, before anything else loads: capture process.ppid while our
+// launcher is (almost certainly) still alive. A launcher killed mid-startup
+// otherwise blinds the PPID watchdog forever (#1185) — see early-ppid.ts.
+require("../mcp/early-ppid");
+// Persist V8 compile artifacts across runs (Node ≥22.8). Every invocation —
+// and every worker thread, which re-requires the whole extraction module
+// graph — skips recompiling unchanged sources. Worth hundreds of ms of
+// worker-boot latency per bulk index; harmless no-op when unavailable.
+try {
+    // eslint-disable-next-line @typescript-eslint/no-require-imports
+    require('node:module').enableCompileCache?.();
+}
+catch { /* cache is best-effort */ }
+const commander_1 = require("commander");
+const path = __importStar(require("path"));
+const fs = __importStar(require("fs"));
+const directory_1 = require("../directory");
+const identifier_segments_1 = require("../search/identifier-segments");
+const worktree_1 = require("../sync/worktree");
+const shimmer_progress_1 = require("../ui/shimmer-progress");
+const glyphs_1 = require("../ui/glyphs");
+const color_1 = require("../ui/color");
+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 command_supervision_1 = require("./command-supervision");
+const extraction_version_1 = require("../extraction/extraction-version");
+const telemetry_1 = require("../telemetry");
+// Value import, but dependency-free by design so `--help` text can name the
+// default port without dragging node:http into every other subcommand; the
+// server itself is loaded lazily inside the `ui` action. See ui-server/constants.
+const constants_1 = require("../ui-server/constants");
+const symbol_lookup_1 = require("../graph/symbol-lookup");
+const query_utils_1 = require("../search/query-utils");
+// Decided once, before `--color`/`--no-color` are stripped from argv below
+// (#1281). Piped/redirected stdout, NO_COLOR, or --no-color -> plain output.
+const COLORS_ENABLED = (0, color_1.ansiColorsEnabled)();
+// Lazy-load heavy modules (Alpha Code Sense, runInstaller) to keep CLI startup fast.
+async function loadAlphaCodeSense() {
+    try {
+        return await Promise.resolve().then(() => __importStar(require('../index')));
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        const [red, reset] = COLORS_ENABLED ? ['\x1b[31m', '\x1b[0m'] : ['', ''];
+        console.error(`${red}${(0, glyphs_1.getGlyphs)().err}${reset} Failed to load Alpha Code Sense 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 @ltm/alpha-cs\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 Alpha Code Sense on Node.js 25.x — V8's turboshaft WASM JIT has a Zone
+// allocator bug that reliably crashes when compiling tree-sitter
+// grammars (see #54, #81, #140). The previous behaviour was a soft
+// console.warn that scrolls off-screen before the OOM crash 30 seconds
+// later, leading to a steady stream of "what is this OOM" reports.
+// Hard-exit before any WASM work; allow override via env var for users
+// who patched V8 themselves or want to test a future fix.
+const nodeVersion = process.versions.node;
+const nodeMajor = parseInt(nodeVersion.split('.')[0] ?? '0', 10);
+if (nodeMajor >= 25) {
+    process.stderr.write((0, node_version_check_1.buildNode25BlockBanner)(nodeVersion) + '\n');
+    if (!process.env.CODEGRAPH_ALLOW_UNSAFE_NODE) {
+        process.exit(1);
+    }
+    // Override active — banner shown for visibility, continuing.
+}
+// 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.CODEGRAPH_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 `codegraph version` subcommand is registered further down so
+    // the affordance also shows up in `codegraph --help`.
+    const firstArg = process.argv[2];
+    if (firstArg === '-v' || firstArg === '-version') {
+        console.log(packageJson.version);
+        return;
+    }
+    // =============================================================================
+    // ANSI Color Helpers (avoid chalk ESM issues)
+    // =============================================================================
+    // `--color` / `--no-color` are global and position-independent — they were
+    // already read by ansiColorsEnabled() at module load, so strip them before
+    // commander parses (a subcommand would otherwise reject the unknown flag).
+    process.argv = process.argv.filter((a) => a !== '--color' && a !== '--no-color');
+    const colors = COLORS_ENABLED
+        ? {
+            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',
+        }
+        : {
+            reset: '',
+            bold: '',
+            dim: '',
+            red: '',
+            green: '',
+            yellow: '',
+            blue: '',
+            cyan: '',
+            white: '',
+            gray: '',
+        };
+    const chalk = {
+        bold: (s) => `${colors.bold}${s}${colors.reset}`,
+        dim: (s) => `${colors.dim}${s}${colors.reset}`,
+        red: (s) => `${colors.red}${s}${colors.reset}`,
+        green: (s) => `${colors.green}${s}${colors.reset}`,
+        yellow: (s) => `${colors.yellow}${s}${colors.reset}`,
+        blue: (s) => `${colors.blue}${s}${colors.reset}`,
+        cyan: (s) => `${colors.cyan}${s}${colors.reset}`,
+        white: (s) => `${colors.white}${s}${colors.reset}`,
+        gray: (s) => `${colors.gray}${s}${colors.reset}`,
+    };
+    program
+        .name('codegraph')
+        .description('Code intelligence and knowledge graph for any codebase')
+        .version(packageJson.version)
+        // Parsed manually before commander runs (any argv position works); declared
+        // here so they show up in --help. NO_COLOR / FORCE_COLOR env vars are also
+        // honored, and piped output defaults to no color (#1281).
+        .option('--color', 'force ANSI colors even when stdout is not a TTY')
+        .option('--no-color', 'disable ANSI colors (NO_COLOR env is also honored)');
+    // 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.CODEGRAPH_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 Alpha Code Sense project
+     * (must have .alpha-cs/codegraph.db, not just .alpha-cs/lessons.db)
+     */
+    function resolveProjectPath(pathArg) {
+        const absolutePath = path.resolve(pathArg || process.cwd());
+        // If exact path is initialized (has codegraph.db), use it
+        if ((0, directory_1.isInitialized)(absolutePath)) {
+            return absolutePath;
+        }
+        // Walk up to find nearest parent with Alpha Code Sense initialized
+        // Note: findNearestAlphaCsRoot finds any .codegraph folder, but we need one with codegraph.db
+        let current = absolutePath;
+        const root = path.parse(current).root;
+        while (current !== root) {
+            const parent = path.dirname(current);
+            if (parent === current)
+                break;
+            current = parent;
+            if ((0, directory_1.isInitialized)(current)) {
+                return current;
+            }
+        }
+        // Not found - return original path (will fail later with helpful error)
+        return absolutePath;
+    }
+    /**
+     * Format a number with commas
+     */
+    function formatNumber(n) {
+        return n.toLocaleString();
+    }
+    /**
+     * Format duration in milliseconds to human readable
+     */
+    function formatDuration(ms) {
+        if (ms < 1000) {
+            return `${ms}ms`;
+        }
+        const seconds = ms / 1000;
+        if (seconds < 60) {
+            return `${seconds.toFixed(1)}s`;
+        }
+        const minutes = Math.floor(seconds / 60);
+        const remainingSeconds = seconds % 60;
+        return `${minutes}m ${remainingSeconds.toFixed(0)}s`;
+    }
+    // Shimmer progress renderer (runs in a worker thread for smooth animation)
+    // Imported at top of file from '../ui/shimmer-progress'
+    /**
+     * Create a plain-text progress callback for --verbose mode.
+     * No animations, no ANSI tricks — just timestamped lines to stdout.
+     */
+    function createVerboseProgress() {
+        let lastPhase = '';
+        let lastPct = -1;
+        const startTime = Date.now();
+        return (progress) => {
+            const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
+            if (progress.phase !== lastPhase) {
+                lastPhase = progress.phase;
+                lastPct = -1;
+                console.log(`[${elapsed}s] Phase: ${progress.phase}`);
+            }
+            if (progress.total > 0) {
+                const pct = Math.floor((progress.current / progress.total) * 100);
+                // Log every 5% to keep output manageable
+                if (pct >= lastPct + 5 || progress.current === progress.total) {
+                    lastPct = pct;
+                    console.log(`[${elapsed}s]   ${progress.current}/${progress.total} (${pct}%)${progress.currentFile ? ` ${(0, glyphs_1.getGlyphs)().dash} ${progress.currentFile}` : ''}`);
+                }
+            }
+            else if (progress.current > 0) {
+                // Scanning phase (no total yet) — log periodically
+                if (progress.current % 1000 === 0 || progress.current === 1) {
+                    console.log(`[${elapsed}s]   ${formatNumber(progress.current)} files found`);
+                }
+            }
+        };
+    }
+    /**
+     * Print success message
+     */
+    function success(message) {
+        console.log(chalk.green((0, glyphs_1.getGlyphs)().ok) + ' ' + message);
+    }
+    /**
+     * Print error message
+     */
+    function error(message) {
+        console.error(chalk.red((0, glyphs_1.getGlyphs)().err) + ' ' + message);
+    }
+    /**
+     * Print info message
+     */
+    function info(message) {
+        console.log(chalk.blue((0, glyphs_1.getGlyphs)().info) + ' ' + message);
+    }
+    /**
+     * Print warning message
+     */
+    function warn(message) {
+        console.log(chalk.yellow((0, glyphs_1.getGlyphs)().warn) + ' ' + message);
+    }
+    /** "not found" (+ optional did-you-mean) when no exact symbol matches. */
+    function formatSymbolNotFound(symbol, fuzzyNames) {
+        const suggestions = [...new Set(fuzzyNames.filter((n) => n !== symbol))].slice(0, 3);
+        if (suggestions.length === 0)
+            return `Symbol "${symbol}" not found`;
+        return `Symbol "${symbol}" not found — did you mean: ${suggestions.join(', ')}?`;
+    }
+    /** Compact node shape retained by the CLI's existing JSON lists. */
+    function cliNode(node) {
+        return { name: node.name, kind: node.kind, filePath: node.filePath, startLine: node.startLine };
+    }
+    /** Attribute a group's edges to every overload of this definition. */
+    function cliDefinition(group) {
+        const head = group[0];
+        return {
+            definition: { ...cliNode(head), id: head.id, qualifiedName: head.qualifiedName, language: head.language },
+            roots: group.map((node) => node.id),
+        };
+    }
+    /**
+     * Print indexing results using clack log methods
+     */
+    function printIndexResult(clack, result, projectPath) {
+        const hasErrors = result.filesErrored > 0;
+        const parseWarnings = result.errors.filter((e) => e.code === 'parse_error' && e.severity === 'warning');
+        // 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 ${formatDuration(result.durationMs)}`);
+            // Warning-only parse failures keep indexing successful, but must be visible.
+            for (const warning of parseWarnings) {
+                clack.log.warn(warning.message);
+            }
+            // A PARTIAL index (files silently dropped mid-pipeline) must not pass
+            // as a clean run — it's the difference between "indexed the repo" and
+            // "indexed most of the repo, quietly". Only the completeness
+            // reconciliation warning; per-file extractor warnings stay in the
+            // error-code summary below.
+            for (const w of result.errors.filter((e) => e.code === 'index_partial')) {
+                clack.log.warn(w.message);
+            }
+            // Files salvaged from comment-stripped source after repeated parser
+            // failures are indexed but possibly incomplete — say so here, or the run
+            // reads as fully clean and the index quietly disagrees with a later
+            // re-parse of the same bytes (#1565).
+            const salvaged = result.errors.filter((e) => e.code === 'salvaged_stripped');
+            if (salvaged.length > 0) {
+                const sample = salvaged.slice(0, 3).map((e) => e.filePath).filter(Boolean).join(', ');
+                const more = salvaged.length > 3 ? ', ...' : '';
+                clack.log.warn(`${formatNumber(salvaged.length)} file(s) indexed from comment-stripped source after repeated parse failures ${(0, glyphs_1.getGlyphs)().dash} symbols may be incomplete (${sample}${more})`);
+            }
+        }
+        else if (hasErrors) {
+            clack.log.error(`Indexing failed ${(0, glyphs_1.getGlyphs)().dash} all ${formatNumber(result.filesErrored)} files had errors`);
+        }
+        else if (result.filesSkippedUnsupported) {
+            // A project Alpha Code Sense has no grammar for used to be indistinguishable from
+            // an empty one: same message, same `complete` state, same exit 0. Say which
+            // files were there and that the graph is empty on purpose, so nobody — and
+            // no agent trusting the graph — reads silence as "this code doesn't exist"
+            // (#1502).
+            const top = (result.topUnsupportedExtensions ?? [])
+                .map(e => `${e.ext} (${formatNumber(e.count)})`)
+                .join(', ');
+            clack.log.warn(`No supported source files found ${(0, glyphs_1.getGlyphs)().dash} ${formatNumber(result.filesSkippedUnsupported)} file(s) present, none in a language Alpha Code Sense indexes`
+                + (top ? `: ${top}` : ''));
+            clack.log.info('Alpha Code Sense is inactive for this workspace — searches will return nothing. Use your own file tools here.');
+        }
+        else {
+            clack.log.warn('No files found to index');
+        }
+        if (hasErrors) {
+            const errorsByCode = new Map();
+            for (const err of result.errors) {
+                if (err.severity === 'error') {
+                    const code = err.code || 'unknown';
+                    errorsByCode.set(code, (errorsByCode.get(code) || 0) + 1);
+                }
+            }
+            const codeLabels = {
+                parse_error: 'files failed to parse',
+                read_error: 'files could not be read',
+                size_exceeded: 'files exceeded size limit',
+                path_traversal: 'blocked paths',
+                unsupported_language: 'unsupported language',
+                parser_error: 'parser initialization failures',
+            };
+            const breakdown = Array.from(errorsByCode)
+                .map(([code, count]) => `${formatNumber(count)} ${codeLabels[code] || code}`)
+                .join('\n');
+            clack.note(breakdown, 'Error breakdown');
+            if (projectPath) {
+                writeErrorLog(projectPath, result.errors);
+                clack.log.info('See .alpha-cs/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) {
+            // No hard errors. Salvaged-file warnings still belong in the log — it
+            // carries the per-file detail behind the one-line summary above.
+            if (result.errors.some((e) => e.code === 'salvaged_stripped')) {
+                writeErrorLog(projectPath, result.errors);
+                clack.log.info('See .alpha-cs/errors.log for details');
+            }
+            else {
+                const logPath = path.join((0, directory_1.getAlphaCsDir)(projectPath), 'errors.log');
+                if (fs.existsSync(logPath)) {
+                    fs.unlinkSync(logPath);
+                }
+            }
+        }
+    }
+    /**
+     * When an `init`/`index` produced an EMPTY graph and the reason is that the
+     * project's own `.gitignore` excludes nested git repositories — the "super-repo
+     * gitignores its child repos" layout (#1156), where `init` at the parent
+     * correctly indexes ~nothing while `init` inside each child works — name those
+     * repos and offer to index them. An interactive terminal gets a yes/no prompt
+     * that writes `includeIgnored` to codegraph.json and re-indexes; a
+     * non-interactive run just prints the one-line opt-in snippet. The caller gates
+     * this on `nodesCreated === 0`, so a project that DID index real content is
+     * never nagged about the gitignored reference clones it deliberately keeps out
+     * (#970, #1065). Best-effort throughout: detection never breaks the command.
+     */
+    async function offerIndexIgnoredRepos(clack, projectPath, reindex, opts) {
+        let repos;
+        try {
+            const { findUnindexedIgnoredRepos } = await Promise.resolve().then(() => __importStar(require('../extraction')));
+            repos = findUnindexedIgnoredRepos(projectPath);
+        }
+        catch {
+            return; // detection is advisory — never let it break the command
+        }
+        if (repos.length === 0)
+            return;
+        const { PROJECT_CONFIG_FILENAME } = await Promise.resolve().then(() => __importStar(require('../project-config')));
+        const isOne = repos.length === 1;
+        const SHOWN = 6;
+        const names = repos.slice(0, SHOWN).map((r) => r.replace(/\/$/, ''));
+        const extra = repos.length > SHOWN ? ` (+${formatNumber(repos.length - SHOWN)} more)` : '';
+        const snippet = `{ "includeIgnored": [${repos.map((p) => JSON.stringify(p)).join(', ')}] }`;
+        clack.log.warn(`Your .gitignore excludes ${isOne ? 'a nested git repository' : `${formatNumber(repos.length)} nested git repositories`} here, ` +
+            `so ${isOne ? 'it was' : 'they were'} not indexed: ${names.join(', ')}${extra}.`);
+        const manualHint = () => {
+            clack.log.info(`If ${isOne ? "it's" : "they're"} your code, add ${isOne ? 'it' : 'them'} to ${PROJECT_CONFIG_FILENAME} and re-index:`);
+            clack.log.info(`  ${snippet}`);
+        };
+        if (!opts.interactive || !process.stdin.isTTY) {
+            manualHint();
+            return;
+        }
+        const yes = await clack.confirm({
+            message: `Index ${isOne ? 'it' : `these ${formatNumber(repos.length)}`} now? Adds ${isOne ? 'it' : 'them'} to ${PROJECT_CONFIG_FILENAME}.`,
+            initialValue: true,
+        });
+        if (clack.isCancel(yes) || !yes) {
+            manualHint();
+            return;
+        }
+        let added;
+        try {
+            const { addIncludeIgnoredPatterns } = await Promise.resolve().then(() => __importStar(require('../project-config')));
+            added = addIncludeIgnoredPatterns(projectPath, repos);
+        }
+        catch (err) {
+            clack.log.error(`Could not update ${PROJECT_CONFIG_FILENAME}: ${err instanceof Error ? err.message : String(err)}`);
+            manualHint();
+            return;
+        }
+        clack.log.success(`Added ${formatNumber(added)} ${added === 1 ? 'entry' : 'entries'} to ${PROJECT_CONFIG_FILENAME} ${(0, glyphs_1.getGlyphs)().dash} re-indexing…`);
+        const result = await reindex();
+        printIndexResult(clack, result, projectPath);
+        return result;
+    }
+    /**
+     * Write detailed error log to .alpha-cs/errors.log
+     */
+    function writeErrorLog(projectPath, errors) {
+        const cgDir = (0, directory_1.getAlphaCsDir)(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 = [
+            `Alpha Code Sense 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
+    // =============================================================================
+    /**
+     * The `init` flow — shared by `codegraph init` and `codegraph install --init`
+     * (#1578): refuse an unsafe root, create `.alpha-cs/`, build the initial
+     * index under supervision, then the post-index offers. `yes` makes every
+     * offer non-interactive (defaults only), so a container / CI bootstrap never
+     * blocks on a prompt. An unsafe root sets `process.exitCode = 1` and returns
+     * (no `--force` is implied by any caller); an index failure exits 1.
+     */
+    async function runInit(projectPath, options) {
+        const clack = await importESM('@clack/prompts');
+        clack.intro('Initializing Alpha Code Sense');
+        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 "codegraph index" to re-index or "codegraph sync" to update');
+                try {
+                    const { offerWatchFallback } = await Promise.resolve().then(() => __importStar(require('../installer')));
+                    await offerWatchFallback(clack, projectPath, { yes: options.yes });
+                }
+                catch { /* non-fatal */ }
+                clack.outro('');
+                return;
+            }
+            const { default: AlphaCodeSense, getDatabasePath } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.init(projectPath, { index: false });
+            clack.log.success(`Initialized in ${projectPath}`);
+            // Indexing runs by default now. The legacy -i/--index flag is still
+            // accepted (so existing muscle memory and scripts don't break) but is a
+            // no-op — initializing always builds the initial index.
+            // Supervise the index: self-terminate if orphaned or wedged (#999).
+            // The DB + WAL paths let the liveness watchdog tell a slow store on
+            // degraded storage from a true wedge (#1231).
+            // A closure so we can re-run the exact same supervised, progress-rendered
+            // index if the user opts gitignored child repos in below (#1156).
+            const dbPath = getDatabasePath(projectPath);
+            const runIndex = async () => {
+                const supervision = (0, command_supervision_1.installCommandSupervision)('init', { progressPaths: [dbPath, `${dbPath}-wal`] });
+                try {
+                    if (options.verbose) {
+                        return await cg.indexAll({ onProgress: createVerboseProgress(), verbose: true });
+                    }
+                    process.stdout.write(`${colors.dim}${(0, glyphs_1.getGlyphs)().rail}${colors.reset}\n`);
+                    const progress = (0, shimmer_progress_1.createShimmerProgress)();
+                    const r = await cg.indexAll({ onProgress: progress.onProgress });
+                    await progress.stop();
+                    return r;
+                }
+                finally {
+                    supervision.stop();
+                }
+            };
+            const result = await runIndex();
+            printIndexResult(clack, result, projectPath);
+            await recordIndexTelemetry(cg, result);
+            // An empty graph at a git super-repo usually means `.gitignore` excludes
+            // the child repos that hold the code — surface them and offer to opt in
+            // rather than leaving the user with a silent 0-node "Done". (#1156)
+            // Under --yes the offer prints its one-line opt-in snippet instead of
+            // prompting (same as a non-TTY run).
+            if (result.nodesCreated === 0) {
+                await offerIndexIgnoredRepos(clack, projectPath, runIndex, { interactive: !options.yes });
+            }
+            try {
+                const { offerWatchFallback } = await Promise.resolve().then(() => __importStar(require('../installer')));
+                await offerWatchFallback(clack, projectPath, { yes: options.yes });
+            }
+            catch { /* non-fatal */ }
+            clack.outro('Done');
+            cg.destroy();
+        }
+        catch (err) {
+            clack.log.error(`Failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    }
+    /**
+     * codegraph init [path]
+     */
+    program
+        .command('init [path]')
+        .description('Initialize Alpha Code Sense 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')
+        .option('-y, --yes', 'Non-interactive: skip every prompt and take the defaults (for scripts / CI / container bootstraps)')
+        .action(async (pathArg, options) => {
+        await runInit(path.resolve(pathArg || process.cwd()), options);
+    });
+    /**
+     * codegraph uninit [path]
+     */
+    program
+        .command('uninit [path]')
+        .description('Remove Alpha Code Sense from a project (deletes .alpha-cs/ directory)')
+        .option('-f, --force', 'Skip confirmation prompt')
+        .action(async (pathArg, options) => {
+        const projectPath = resolveProjectPath(pathArg);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                warn(`Alpha Code Sense 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 Alpha Code Sense data. Continue? (y/N) `), resolve);
+                });
+                rl.close();
+                if (answer.toLowerCase() !== 'y') {
+                    info('Cancelled');
+                    return;
+                }
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = AlphaCodeSense.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 Alpha Code Sense 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);
+        }
+    });
+    /**
+     * codegraph 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) => {
+        // An EXPLICIT path names the project to rebuild — it is never a hint to go
+        // looking for one. resolveProjectPath walks up to the nearest initialized
+        // ancestor, which is right for `codegraph query` run from a subdirectory,
+        // but for a full re-index it silently rebuilt the parent's graph under a
+        // normal "Done" when <path> had no index of its own (#1524). Only a bare
+        // `codegraph index` (cwd) may resolve upward.
+        const projectPath = pathArg ? path.resolve(pathArg) : resolveProjectPath();
+        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(`Alpha Code Sense not initialized in ${projectPath}`);
+                const ancestor = pathArg ? resolveProjectPath(pathArg) : projectPath;
+                if (ancestor !== projectPath) {
+                    info(`The nearest initialized project is ${ancestor} — pass that path to rebuild it, or run "codegraph init" in ${projectPath} to index it on its own.`);
+                }
+                else {
+                    info('Run "codegraph init" first');
+                }
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense, getDatabasePath } = await loadAlphaCodeSense();
+            // `index` is a FULL re-index — identical to a fresh `init`. RECREATE the
+            // database from scratch (discard .alpha-cs/codegraph.db + its WAL) rather
+            // than opening the old graph and DELETE-ing every row. The clear-then-index
+            // approach reported "0 nodes" without the clear (#874); the recreate keeps
+            // that fixed AND avoids the failure mode where, on a large or pre-fix
+            // poisoned index, the per-row FTS delete churn wedged the main thread long
+            // enough to trip the liveness watchdog before scanning even began (#1067).
+            // recreate() hands back a fresh, empty instance — no clear() needed. For
+            // fast incremental updates use `sync`.
+            const cg = await AlphaCodeSense.recreate(projectPath);
+            // Supervise the indexer: self-terminate if orphaned (parent shim killed)
+            // or if the main thread wedges — neither was guarded on this path (#999).
+            // The DB + WAL paths let the liveness watchdog tell a slow store on
+            // degraded storage from a true wedge (#1231).
+            const dbPath = getDatabasePath(projectPath);
+            const supervision = (0, command_supervision_1.installCommandSupervision)('index', { progressPaths: [dbPath, `${dbPath}-wal`] });
+            try {
+                if (options.quiet) {
+                    // Quiet mode: no UI, just run against the freshly-recreated graph.
+                    const result = await cg.indexAll();
+                    if (!result.success)
+                        process.exit(1);
+                    cg.destroy();
+                    return;
+                }
+                const clack = await importESM('@clack/prompts');
+                clack.intro('Indexing project');
+                // A closure so a re-index (after opting gitignored child repos in, #1156)
+                // renders identically. Supervision already wraps the whole command.
+                const renderIndex = async () => {
+                    if (options.verbose) {
+                        return await cg.indexAll({ onProgress: createVerboseProgress(), verbose: true });
+                    }
+                    process.stdout.write(`${colors.dim}${(0, glyphs_1.getGlyphs)().rail}${colors.reset}\n`);
+                    const progress = (0, shimmer_progress_1.createShimmerProgress)();
+                    const r = await cg.indexAll({ onProgress: progress.onProgress });
+                    await progress.stop();
+                    return r;
+                };
+                const result = await renderIndex();
+                printIndexResult(clack, result, projectPath);
+                await recordIndexTelemetry(cg, result);
+                // Empty graph at a git super-repo → likely `.gitignore`d child repos;
+                // name them and offer to opt in instead of a silent 0-node result (#1156).
+                let finalResult = result;
+                if (result.nodesCreated === 0) {
+                    finalResult = (await offerIndexIgnoredRepos(clack, projectPath, renderIndex, { interactive: true })) ?? result;
+                }
+                if (!finalResult.success) {
+                    process.exit(1);
+                }
+                clack.outro('Done');
+                cg.destroy();
+            }
+            finally {
+                supervision.stop();
+            }
+        }
+        catch (err) {
+            error(`Failed to index: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph sync [path]
+     */
+    program
+        .command('sync [path]')
+        .description('Sync changes since last index')
+        .option('-q, --quiet', 'Suppress output (for git hooks)')
+        .action(async (pathArg, options) => {
+        const projectPath = resolveProjectPath(pathArg);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                if (!options.quiet) {
+                    error(`Alpha Code Sense not initialized in ${projectPath}`);
+                }
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            if (options.quiet) {
+                await cg.sync();
+                cg.destroy();
+                return;
+            }
+            const clack = await importESM('@clack/prompts');
+            clack.intro('Syncing Alpha Code Sense');
+            process.stdout.write(`${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);
+        }
+    });
+    /**
+     * ltm-alpha-cs 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.getAlphaCsDir)(projectPath),
+                        lastIndexed: null,
+                    }));
+                    return;
+                }
+                console.log(chalk.bold('\nCodeGraph Status\n'));
+                info(`Project: ${projectPath}`);
+                warn('Not initialized');
+                info('Run "codegraph init" to initialize');
+                return;
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.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();
+            const indexState = cg.getIndexState();
+            // Zero on a healthy index; non-zero at rest means a resolution pass was
+            // interrupted, so some files' call edges are missing (#1187).
+            const pendingRefs = cg.getPendingReferenceCount();
+            // JSON output mode
+            if (options.json) {
+                const lastIndexedMs = cg.getLastIndexedAt();
+                console.log(JSON.stringify({
+                    initialized: true,
+                    version: packageJson.version,
+                    projectPath,
+                    indexPath: (0, directory_1.getAlphaCsDir)(projectPath),
+                    lastIndexed: lastIndexedMs != null ? new Date(lastIndexedMs).toISOString() : null,
+                    fileCount: stats.fileCount,
+                    nodeCount: stats.nodeCount,
+                    edgeCount: stats.edgeCount,
+                    dbSizeBytes: stats.dbSizeBytes,
+                    walSizeBytes: stats.walSizeBytes,
+                    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,
+                        // 'complete' | 'partial' (files silently dropped) | 'indexing'
+                        // (a run was killed mid-index — the index is truncated) |
+                        // 'failed' | null (predates the marker).
+                        state: indexState,
+                        // References awaiting resolution. Non-zero at rest means an
+                        // interrupted resolution pass left edges missing; the next
+                        // sync sweeps them (#1187).
+                        pendingRefs,
+                    },
+                }));
+                cg.destroy();
+                return;
+            }
+            console.log(chalk.bold('\nCodeGraph Status\n'));
+            // Project info
+            console.log(chalk.cyan('Project:'), projectPath);
+            if (worktreeMismatch) {
+                warn((0, worktree_1.worktreeMismatchWarning)(worktreeMismatch));
+            }
+            if (indexState === 'indexing') {
+                warn('The last index run never finished (killed mid-index?) — the index is truncated. Re-run "codegraph index".');
+            }
+            else if (indexState === 'partial') {
+                warn('The last index run silently dropped files — the index is partial. Re-run "codegraph index".');
+            }
+            else if (indexState === 'failed') {
+                warn('The last index run failed — results may be incomplete. Re-run "codegraph index".');
+            }
+            if (pendingRefs > 0) {
+                warn(`${formatNumber(pendingRefs)} references from an interrupted run are awaiting resolution — some callers/impact edges are missing. Run "codegraph sync" to resolve them.`);
+            }
+            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:   ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`);
+            // Surface the WAL sidecar (#1431): a WAL that dwarfs the DB at rest is
+            // the killed-session leak — invisible before this line, it only showed
+            // up as a mysteriously full disk. open() above already kicked off the
+            // automatic heal for the oversized case.
+            if (stats.walSizeBytes > 0) {
+                const { WAL_HEAL_THRESHOLD_BYTES } = await Promise.resolve().then(() => __importStar(require('../db/index')));
+                const oversized = stats.walSizeBytes > Math.max(WAL_HEAL_THRESHOLD_BYTES, stats.dbSizeBytes);
+                const walLabel = `${(stats.walSizeBytes / 1024 / 1024).toFixed(2)} MB`;
+                console.log(`  WAL Size:  ${oversized ? chalk.yellow(walLabel) : walLabel}`);
+                if (oversized) {
+                    warn('The write-ahead log is larger than the database — killed sessions left it behind. It is reclaimed automatically on open; if it persists across runs, another live Alpha Code Sense process is holding it.');
+                }
+            }
+            // 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:   ${changes.removed.length} files`);
+                }
+                info('Run "codegraph sync" to update the index');
+            }
+            else {
+                success('Index is up to date');
+            }
+            console.log();
+            // Re-index hint: the index was built by an older engine than the one now
+            // running, so a rebuild would add data a migration can't backfill.
+            if (reindexRecommended) {
+                const builtWith = buildInfo.version ? `v${buildInfo.version.replace(/^v/, '')}` : 'an earlier version';
+                warn(`Index was built by ${builtWith}; re-index to pick up this engine's improvements.`);
+                info('Run "codegraph index" (full rebuild) or "codegraph sync"');
+                console.log();
+            }
+            cg.destroy();
+        }
+        catch (err) {
+            error(`Failed to get status: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph query <search>
+     */
+    program
+        .command('query <search>')
+        .description('Search for symbols in the codebase')
+        .option('-p, --path <path>', 'Project path')
+        .option('-l, --limit <number>', 'Maximum results', '10')
+        .option('-k, --kind <kind>', 'Filter by node kind (function, class, etc.)')
+        .option('-j, --json', 'Output as JSON')
+        .action(async (search, options) => {
+        const projectPath = resolveProjectPath(options.path);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense not initialized in ${projectPath}`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            const limit = parseInt(options.limit || '10', 10);
+            const rawResults = cg.searchNodes(search, {
+                // Fetch one extra row so the CLI can report a cut without changing the
+                // long-standing bare-array contract of `query --json` (#1639).
+                limit: limit + 1,
+                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 isGen = cg.generatedFilePredicate(rawResults.map((r) => r.node.filePath));
+            const rankedResults = [...rawResults].sort((a, b) => {
+                const aGen = isGen(a.node.filePath) ? 1 : 0;
+                const bGen = isGen(b.node.filePath) ? 1 : 0;
+                return aGen - bGen;
+            });
+            const truncated = rankedResults.length > limit;
+            const results = rankedResults.slice(0, limit);
+            const truncationMessage = `Results truncated at ${limit}; pass --limit to widen.`;
+            if (options.json) {
+                console.log(JSON.stringify(results, null, 2));
+                if (truncated)
+                    console.error(truncationMessage);
+            }
+            else {
+                if (results.length === 0) {
+                    info(`No results found for "${search}"`);
+                }
+                else {
+                    console.log(chalk.bold(`\nSearch Results for "${search}":\n`));
+                    // Results arrive already ranked by relevance, so the order conveys
+                    // it. We don't print the raw score: it's an unbounded BM25/FTS value
+                    // (relative-ranking only), and the old `(score * 100)%` rendered it
+                    // as nonsensical percentages like "12042%" (#1045). The MCP search
+                    // tool likewise shows no score. Raw `score` stays in --json output.
+                    for (const result of results) {
+                        const node = result.node;
+                        const location = `${node.filePath}:${node.startLine}`;
+                        console.log(chalk.cyan(node.kind.padEnd(12)) +
+                            chalk.white(node.name));
+                        console.log(chalk.dim(`  ${location}`));
+                        if (node.signature) {
+                            console.log(chalk.dim(`  ${node.signature}`));
+                        }
+                        console.log();
+                    }
+                    if (truncated)
+                        console.log(chalk.dim(truncationMessage));
+                }
+            }
+            cg.destroy();
+        }
+        catch (err) {
+            error(`Search failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph 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(`Alpha Code Sense isn't available here — no .alpha-cs/ 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 Alpha Code Sense with 'codegraph init'.)`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.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: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph context <task...>
+     *
+     * The CLI face of the public `buildContext` API (ContextBuilder): FTS entry
+     * points + graph expansion + code blocks, formatted as markdown or JSON.
+     * Advertised in the usage header since the first release but never actually
+     * registered (#1611); external integrations (e.g. Memorix) invoke it as
+     * `codegraph context --path <root> --format json --max-nodes 8 --no-code <task>`.
+     */
+    program
+        .command('context <task...>')
+        .description('Build context for a task: relevant symbols, relationships, and code blocks')
+        .option('-p, --path <path>', 'Project path')
+        .option('-f, --format <format>', 'Output format: markdown or json', 'markdown')
+        .option('-n, --max-nodes <number>', 'Maximum number of symbols to include')
+        .option('--no-code', 'Omit code blocks (structure only)')
+        .action(async (taskParts, options) => {
+        const projectPath = resolveProjectPath(options.path);
+        const format = options.format ?? 'markdown';
+        if (format !== 'markdown' && format !== 'json') {
+            error(`Unknown format "${options.format}" — use "markdown" or "json".`);
+            process.exit(1);
+        }
+        let maxNodes;
+        if (options.maxNodes !== undefined) {
+            maxNodes = parseInt(options.maxNodes, 10);
+            if (Number.isNaN(maxNodes) || maxNodes < 1) {
+                error(`--max-nodes expects a positive integer, got "${options.maxNodes}".`);
+                process.exit(1);
+            }
+        }
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense not initialized in ${projectPath}`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            const result = await cg.buildContext(taskParts.join(' '), {
+                format,
+                includeCode: options.code !== false,
+                ...(maxNodes !== undefined ? { maxNodes } : {}),
+            });
+            // Both supported formats return a formatted string; print it verbatim so
+            // `--format json` stays machine-parseable on stdout (error()/warnings go
+            // to stderr only).
+            console.log(typeof result === 'string' ? result : JSON.stringify(result, null, 2));
+            cg.destroy();
+        }
+        catch (err) {
+            error(`Context build failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph 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 Alpha Code Sense (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 Alpha Code Sense 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.ALPHA_CS_NO_PROMPT_HOOK === '1' || process.env.CODEGRAPH_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 telemetry: how often each tier fires vs. no-ops — counter names
+            // only, NEVER prompt content (see TELEMETRY.md). This is the data that
+            // turns "is the gate any good" from vibes into a measured recall rate.
+            const gate = (outcome) => {
+                try {
+                    (0, telemetry_1.getTelemetry)().recordUsage('cli_command', `prompt-hook-gate-${outcome}`, true);
+                }
+                catch { /* never break the hook */ }
+            };
+            // Gate, tiered by confidence (#994, #1126):
+            //   HIGH   — a structural keyword (any covered language), or a code-shaped
+            //            token verified in the index → full explore injection.
+            //   MEDIUM — no keyword/token, but prose words match indexed symbol-name
+            //            SEGMENTS ("state machine" → OrderStateMachine, in any
+            //            language): inject a short list of the matching symbols and
+            //            let the AGENT write the explore query — the graph-derived
+            //            tier, no vocabulary involved.
+            //   silent — nothing verified. Every other prompt ("fix this typo")
+            //            stays a zero-cost no-op.
+            // Keywords fire on their own; a token or prose word is only a CANDIDATE
+            // verified against the graph below, so a tech brand ("JavaScript") that
+            // merely looks like code doesn't inject spurious context.
+            const keyworded = (0, directory_1.hasStructuralKeyword)(prompt);
+            const codeTokens = keyworded ? [] : (0, directory_1.extractCodeTokens)(prompt);
+            const proseWords = keyworded ? [] : (0, identifier_segments_1.extractProseCandidates)(prompt);
+            if (!keyworded && codeTokens.length === 0 && proseWords.length === 0) {
+                gate('noop-shape');
+                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) {
+                gate('noop-no-index');
+                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: "${p}"`).join('\n')}\n`;
+            if (plan.exploreRoot) {
+                const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+                const cg = await AlphaCodeSense.open(plan.exploreRoot);
+                try {
+                    const others = plan.nudgeProjects.length
+                        ? `\n${nudge(plan.nudgeProjects, 'Other indexed projects in this workspace — pass projectPath to query them:')}`
+                        : '';
+                    // Tier decision against THIS index (issue #994 follow-up: candidates
+                    // must be real here — a brand name or prose about another domain
+                    // must not inject). Keyword-bearing prompts skip verification — the
+                    // keyword is signal enough.
+                    const tokenVerified = !keyworded && codeTokens.some((t) => cg.getNodesByName(t).length > 0);
+                    if (keyworded || tokenVerified) {
+                        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.
+                            // Claude Code shows hook stdout inline only up to 10,000 characters;
+                            // above that it persists the output to a file and the model sees a
+                            // 2 KB preview (#1694). PROMPT_HOOK_INJECTION_MAX (9,000) leaves
+                            // room for the wrapper and the projectPath nudge lines below.
+                            const body = (0, directory_1.capPromptHookInjection)(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';
+                            process.stdout.write(`<codegraph_context note="Structural context from Alpha Code Sense for this prompt — treat returned source as already read; ${more}.">\n${body}${others}\n</codegraph_context>\n`);
+                            gate(keyworded ? 'high-keyword' : 'high-token');
+                        }
+                        else {
+                            // A high-* outcome must mean context was actually delivered —
+                            // the funnel's noop-vs-high split is how gate recall is
+                            // measured (#1143). An explore error or empty result is a
+                            // delivery failure, not a gate success.
+                            gate(keyworded ? 'noop-explore-keyword' : 'noop-explore-token');
+                        }
+                        return;
+                    }
+                    // MEDIUM: prose words → symbol-name segments, co-occurrence/rarity
+                    // scored, each hit re-verified to exist (see getSegmentMatches). The
+                    // payload names the symbols but does NOT run explore — the agent owns
+                    // the query where the hook's confidence is only "these are related".
+                    //
+                    // A database indexed before the vocab table existed starts with it
+                    // EMPTY, and only sync() backfills it — which this hook never runs
+                    // (#1142). Heal it here: on a populated vocab this is one SELECT;
+                    // the actual backfill is a one-time batched pass whose cost the MCP
+                    // server's own catch-up sync usually pays first (it runs at every
+                    // session start). A distinct noop outcome keeps a dormant vocab
+                    // from polluting the noop-unverified recall signal.
+                    const vocabReady = await cg.healSegmentVocabIfEmpty().catch(() => false);
+                    if (!vocabReady) {
+                        gate('noop-vocab-empty');
+                        return;
+                    }
+                    const related = cg.getSegmentMatches(proseWords);
+                    if (related.length === 0) {
+                        gate('noop-unverified');
+                        return;
+                    }
+                    const lines = related
+                        .map((m) => `  - ${m.name} (${m.kind} — ${m.filePath}:${m.startLine})`)
+                        .join('\n');
+                    const exampleQuery = related.slice(0, 3).map((m) => m.name).join(' ');
+                    const projectHint = plan.viaSubScan ? ` with projectPath: "${plan.exploreRoot}"` : '';
+                    process.stdout.write(`<codegraph_context note="Alpha Code Sense found indexed symbols matching this prompt — query the graph before searching files.">\n` +
+                        `This project's Alpha Code Sense index contains symbols matching this request:\n${lines}\n` +
+                        `Call codegraph_explore ONCE${projectHint} with the relevant names in one query (e.g. "${exampleQuery}") ` +
+                        `to get their source, call paths, and blast radius — cheaper and more complete than Read/Grep.\n${others}` +
+                        `</codegraph_context>\n`);
+                    gate('medium-segment');
+                }
+                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="Alpha Code Sense is available for this workspace's indexed sub-projects — query one by passing projectPath to codegraph_explore.">\n` +
+                    nudge(plan.nudgeProjects, "This workspace's Alpha Code Sense indexes live in sub-projects. To use Alpha Code Sense, call codegraph_explore with the projectPath of the relevant one:") +
+                    `</codegraph_context>\n`);
+                gate('nudge-projects');
+            }
+        }
+        catch {
+            // Degradable by contract: never surface an error to the prompt pipeline.
+        }
+    });
+    /**
+     * codegraph 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`.
+     *
+     * `name` is OPTIONAL because `--file` (file-read mode) carries no symbol —
+     * a required `<name>` made `codegraph node -f <file>` unreachable (#1044).
+     */
+    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) => {
+        // Need a symbol (positional) OR a file (--file / a path-like positional).
+        // With [name] optional, a bare `codegraph node` reaches here with neither
+        // and must be told what to pass, rather than crashing downstream.
+        if (!name && !options.file) {
+            error("Pass a symbol name (e.g. 'codegraph node parseToken') or a file (e.g. 'codegraph node -f src/auth.ts', or 'codegraph node src/auth.ts').");
+            process.exit(1);
+        }
+        const projectPath = resolveProjectPath(options.path);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense isn't available here — no .alpha-cs/ 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 Alpha Code Sense with 'codegraph init'.)`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.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;
+                    // Symbol mode pinned to a file is still symbol mode — the CLI
+                    // always wants the body, exactly like the bare-symbol branch
+                    // below. Omitting this printed location + trail with no source
+                    // (#1284).
+                    args.includeCode = true;
+                }
+            }
+            else if (name && (name.includes('/') || name.includes('\\'))) {
+                args.file = name.replace(/\\/g, '/');
+            }
+            else if (name) {
+                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);
+        }
+    });
+    /**
+     * codegraph files [path]
+     */
+    program
+        .command('files')
+        .description('Show project file structure from the index')
+        .option('-p, --path <path>', 'Project path')
+        .option('--filter <dir>', 'Filter to files under this directory')
+        .option('--pattern <glob>', 'Filter files matching this glob pattern')
+        .option('--format <format>', 'Output format (tree, flat, grouped)', 'tree')
+        .option('--max-depth <number>', 'Maximum directory depth for tree format')
+        .option('--no-metadata', 'Hide file metadata (language, symbol count)')
+        .option('-j, --json', 'Output as JSON')
+        .action(async (options) => {
+        const projectPath = resolveProjectPath(options.path);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense not initialized in ${projectPath}`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            let files = cg.getFiles();
+            if (files.length === 0) {
+                info('No files indexed. Run "codegraph index" first.');
+                cg.destroy();
+                return;
+            }
+            // Filter by path prefix
+            if (options.filter) {
+                const filter = options.filter;
+                files = files.filter(f => f.path.startsWith(filter) || f.path.startsWith('./' + filter));
+            }
+            // Filter by glob pattern
+            if (options.pattern) {
+                const regex = globToRegex(options.pattern);
+                files = files.filter(f => regex.test(f.path));
+            }
+            if (files.length === 0) {
+                info('No files found matching the criteria.');
+                cg.destroy();
+                return;
+            }
+            // JSON output
+            if (options.json) {
+                const output = files.map(f => ({
+                    path: f.path,
+                    language: f.language,
+                    nodeCount: f.nodeCount,
+                    size: f.size,
+                }));
+                console.log(JSON.stringify(output, null, 2));
+                cg.destroy();
+                return;
+            }
+            const includeMetadata = options.metadata !== false;
+            const format = options.format || 'tree';
+            const maxDepth = options.maxDepth ? parseInt(options.maxDepth, 10) : undefined;
+            // Format output
+            switch (format) {
+                case 'flat':
+                    console.log(chalk.bold(`\nFiles (${files.length}):\n`));
+                    for (const file of files.sort((a, b) => a.path.localeCompare(b.path))) {
+                        if (includeMetadata) {
+                            console.log(`  ${file.path} ${chalk.dim(`(${file.language}, ${file.nodeCount} symbols)`)}`);
+                        }
+                        else {
+                            console.log(`  ${file.path}`);
+                        }
+                    }
+                    break;
+                case 'grouped':
+                    console.log(chalk.bold(`\nFiles by Language (${files.length} total):\n`));
+                    const byLang = new Map();
+                    for (const file of files) {
+                        const existing = byLang.get(file.language) || [];
+                        existing.push(file);
+                        byLang.set(file.language, existing);
+                    }
+                    const sortedLangs = [...byLang.entries()].sort((a, b) => b[1].length - a[1].length);
+                    for (const [lang, langFiles] of sortedLangs) {
+                        console.log(chalk.cyan(`${lang} (${langFiles.length}):`));
+                        for (const file of langFiles.sort((a, b) => a.path.localeCompare(b.path))) {
+                            if (includeMetadata) {
+                                console.log(`  ${file.path} ${chalk.dim(`(${file.nodeCount} symbols)`)}`);
+                            }
+                            else {
+                                console.log(`  ${file.path}`);
+                            }
+                        }
+                        console.log();
+                    }
+                    break;
+                case 'tree':
+                default:
+                    console.log(chalk.bold(`\nProject Structure (${files.length} files):\n`));
+                    printFileTree(files, includeMetadata, maxDepth, chalk);
+                    break;
+            }
+            console.log();
+            cg.destroy();
+        }
+        catch (err) {
+            error(`Failed to list files: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * Normalize a user-supplied file path to the project-relative, forward-slash
+     * form Alpha Code Sense stores in the index. Accepts an absolute path, a `./`-prefixed
+     * path, or Windows back-slashes; an empty string when the input is blank. Used
+     * by `codegraph affected` so `./src/x.ts`, `/abs/repo/src/x.ts`, and
+     * `src/x.ts` all match the same indexed file. (#825)
+     */
+    function normalizeIndexPath(filePath, projectPath) {
+        let f = filePath.trim();
+        if (!f)
+            return '';
+        if (path.isAbsolute(f))
+            f = path.relative(projectPath, f);
+        // Collapse `.`/`..` segments, then force forward slashes and drop a leading
+        // `./` (path.normalize already strips it on POSIX; explicit for Windows).
+        f = path.normalize(f).replace(/\\/g, '/').replace(/^\.\//, '');
+        return f;
+    }
+    /**
+     * Convert glob pattern to regex
+     */
+    function globToRegex(pattern) {
+        const escaped = pattern
+            .replace(/[.+^${}()|[\]\\]/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);
+    }
+    /**
+     * codegraph 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 Alpha Code Sense background daemons — pick one and press enter to stop it')
+        .action(async () => {
+        const { listVerifiedDaemons, stopDaemonAt, stopAllDaemons } = await Promise.resolve().then(() => __importStar(require('../mcp/daemon-registry')));
+        const { runDaemonPicker } = await Promise.resolve().then(() => __importStar(require('../mcp/daemon-manager')));
+        const daemons = await listVerifiedDaemons();
+        if (daemons.length === 0) {
+            info('No Alpha Code Sense 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.findNearestAlphaCsRoot)(process.cwd());
+        if (found) {
+            try {
+                cwdRoot = fs.realpathSync(found);
+            }
+            catch {
+                cwdRoot = found;
+            }
+        }
+        const clack = await importESM('@clack/prompts');
+        clack.intro('Alpha Code Sense daemons');
+        await runDaemonPicker({
+            list: listVerifiedDaemons,
+            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),
+        });
+    });
+    /**
+     * Print the "no index here" guidance.
+     *
+     * The viewer READS an index; it never builds one — indexing stays the user's
+     * decision, exactly as it is for the MCP tools. So a missing index is normal
+     * input, not a failure to apologize for: say what is missing, say the one
+     * command that fixes it, and never print a stack trace.
+     */
+    function printNoIndexGuidance(projectPath) {
+        error(`No Alpha Code Sense index found for ${projectPath}`);
+        console.error('');
+        // getGlyphs() (not a literal em dash): a legacy Windows console decodes raw
+        // UTF-8 with its OEM codepage and renders one as mojibake (#168).
+        console.error(`  The viewer reads an index that already exists ${(0, glyphs_1.getGlyphs)().dash} it never creates one.`);
+        console.error('  To index this project:');
+        console.error('');
+        console.error(`    ${chalk.cyan('codegraph init')}`);
+        console.error('');
+        console.error('  Already indexed somewhere else? Point the viewer at it:');
+        console.error('');
+        console.error(`    ${chalk.cyan('codegraph ui /path/to/indexed/project')}`);
+        console.error('');
+    }
+    /**
+     * codegraph ui [path]  (alias: web)
+     *
+     * The browser reader: serves the built viewer (`dist/viewer/`) over loopback
+     * and opens it. It opens the index for reading and never writes to it, never
+     * indexes, and never changes a line of the project's code. The single thing it
+     * writes is a trail the reader saved, as JSON under `.alpha-cs/ui/trails/`;
+     * `--read-only` turns even that off.
+     *
+     * Deliberately absent from TELEMETRY_FLUSH_COMMANDS above: the command's own
+     * banner tells the user nothing leaves their machine, so it must not be the
+     * thing that triggers a telemetry send. The usage count still buffers locally
+     * like every other quick command.
+     */
+    program
+        .command('ui [path]')
+        .alias('web')
+        .description('Open the Alpha Code Sense viewer in your browser — read your indexed project as a graph')
+        .option('--port <number>', `Port to listen on (default: ${constants_1.DEFAULT_UI_PORT}, or the next free one)`)
+        .option('--no-open', 'Print the URL instead of opening a browser')
+        .option('--read-only', 'Refuse every write — saved trails can be opened but not saved or deleted')
+        .addHelpText('after', `
+Examples:
+  $ codegraph ui                    Read the project you're standing in
+  $ codegraph ui ~/code/my-app      Read a specific indexed project
+  $ codegraph ui --port 8080        Use one specific port (fails if it's taken)
+  $ codegraph ui --no-open          Just print the URL (headless boxes, SSH)
+  $ codegraph web                   Same command under its alias
+
+Pick a symbol and you see who calls it on the left, its source in the middle,
+and what it calls on the right at the height of the line that calls it. Search
+with / (or Cmd-K), click a file path for the file's outline and its imports.
+
+Ask "how does execute reach getFile" (or "execute -> getFile") in the search
+box for the flow between two symbols: one card per hop, opened at the line that
+makes the next call, with dynamic-dispatch hops drawn dashed and named. The Map
+tab draws the whole project by module, with dependencies pointing down.
+
+Never opened this codebase before? The Entry points tab lists the routes with
+the symbols that serve them, the files that run something when they load, the
+tests, and what the most code depends on — and starts a flow from any of them.
+
+The page keeps up with the project while it is open: save a file and it says so
+within about a third of a second, and whatever is on screen re-reads the graph
+when something re-indexes it. It watches for that; it never polls.
+
+Save a walk you want to keep: name the trail and it is written to
+.alpha-cs/ui/trails/ (already gitignored) as plain JSON, listed on the empty
+screen, and reopened at the symbol you left. Hops are remembered by name rather
+than by position, so a saved trail survives re-indexing and says which hop moved
+when one does. Pass --read-only to refuse every write.
+
+The viewer listens on 127.0.0.1 only, so nothing on your network can reach it.
+It opens an index that already exists, never indexes, and never changes a line
+of your code — the one thing it writes is a trail you asked it to save.
+Requests from any other host are refused, and nothing is sent anywhere: no code,
+no paths, no analytics.
+
+Without --port it takes ${constants_1.DEFAULT_UI_PORT}, or the next free port if that one is busy.
+
+Set ${constants_1.BROWSER_ENV}=<command> to choose which browser opens, or
+${constants_1.BROWSER_ENV}=none to never open one.
+`)
+        .action(async (pathArg, options) => {
+        // An explicit --port stays explicit: a scripted `--port 8080` that quietly
+        // lands on 8081 is worse than one that says the port is busy. The default
+        // port is the only one we're free to walk away from.
+        let requestedPort;
+        if (options.port !== undefined) {
+            requestedPort = Number(options.port);
+            if (!Number.isInteger(requestedPort) || requestedPort < 0 || requestedPort > 65535) {
+                error(`--port must be a whole number between 0 and 65535 (got "${options.port}").`);
+                process.exit(1);
+            }
+        }
+        const projectPath = resolveProjectPath(pathArg);
+        // Sensitive-directory refusal before anything opens: the same guard the MCP
+        // entry points use, so `codegraph ui /etc` is turned away here rather than
+        // becoming a browsable view of the system.
+        const { validateProjectPath } = await Promise.resolve().then(() => __importStar(require('../utils')));
+        const rootError = validateProjectPath(projectPath);
+        if (rootError) {
+            error(rootError);
+            process.exit(1);
+        }
+        if (!(0, directory_1.isInitialized)(projectPath)) {
+            printNoIndexGuidance(projectPath);
+            process.exit(1);
+        }
+        const { startUiServer, openBrowser, createGraphApi, ViewerMissingError } = await Promise.resolve().then(() => __importStar(require('../ui-server')));
+        // The JSON API the viewer reads its screens from. It opens the index lazily
+        // on the first request, so a slow first paint is the only cost of mounting
+        // it here rather than after the browser connects.
+        const readOnly = options.readOnly === true;
+        const api = createGraphApi({
+            projectRoot: projectPath,
+            readOnly,
+            readOnlyReason: readOnly
+                ? 'This viewer was started with --read-only, so trails cannot be saved.'
+                : undefined,
+        });
+        let handle;
+        try {
+            handle = await startUiServer({
+                projectRoot: projectPath,
+                port: requestedPort,
+                portFallback: requestedPort === undefined,
+                api: api.handler,
+            });
+        }
+        catch (err) {
+            api.close();
+            // Both failure modes here (viewer assets missing, no port available) carry
+            // their own remediation — print it plainly, never a stack trace.
+            error(err instanceof ViewerMissingError || err instanceof Error ? err.message : String(err));
+            process.exit(1);
+        }
+        console.log('');
+        console.log(chalk.bold('Alpha Code Sense viewer'));
+        console.log('');
+        console.log(`  ${chalk.dim('Reading')}  ${projectPath}`);
+        console.log(`  ${chalk.dim('URL')}      ${chalk.cyan(handle.url)}`);
+        console.log(`  ${chalk.dim('Access')}   this machine only ${(0, glyphs_1.getGlyphs)().dash} ` +
+            (readOnly
+                ? 'read-only, nothing leaves your computer'
+                : 'nothing leaves your computer; saved trails are the only thing written'));
+        console.log('');
+        const opened = options.open === false ? false : openBrowser(handle.url);
+        console.log(opened
+            ? chalk.dim('  Opening your browser... press Ctrl+C to stop.')
+            : chalk.dim('  Open that URL in a browser. Press Ctrl+C to stop.'));
+        console.log('');
+        // The http server keeps the event loop alive on its own; these just make
+        // Ctrl-C hang up live sockets instead of waiting on browser keep-alives.
+        const shutdown = () => {
+            // Release the SQLite handle before the socket: the process should never
+            // exit with a live connection to the user's index.
+            api.close();
+            void handle.close().then(() => process.exit(0));
+        };
+        process.once('SIGINT', shutdown);
+        process.once('SIGTERM', shutdown);
+    });
+    /**
+     * codegraph 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 Alpha Code Sense as an MCP server for AI assistants')
+        .option('-p, --path <path>', 'Project path (optional for MCP mode, uses rootUri from client)')
+        .option('--mcp', 'Run as MCP server (stdio transport)')
+        .option('--no-watch', 'Disable the file watcher (no auto-sync; useful on slow filesystems like WSL2 /mnt drives)')
+        .action(async (options) => {
+        const projectPath = options.path ? resolveProjectPath(options.path) : undefined;
+        // Commander sets watch=false when --no-watch is passed. Route it through
+        // the same env-var chokepoint the watcher and MCP server already honor.
+        if (options.watch === false) {
+            process.env.CODEGRAPH_NO_WATCH = '1';
+        }
+        try {
+            if (options.mcp) {
+                // `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.CODEGRAPH_DAEMON_INTERNAL) {
+                    console.error(chalk.bold('\nCodeGraph 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('codegraph install')}. To check on things:`);
+                    console.error(`  ${chalk.cyan('ltm-alpha-cs status')}   ${chalk.dim('— is this project indexed and healthy?')}`);
+                    console.error(`  ${chalk.cyan('codegraph 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('\nCodeGraph MCP Server\n'));
+                console.error(chalk.blue((0, glyphs_1.getGlyphs)().info) + ' Use --mcp flag to start the MCP server');
+                console.error('\nTo use with Claude Code, add to your MCP configuration:');
+                console.error(chalk.dim(`
+{
+  "mcpServers": {
+    "codegraph": {
+      "command": "codegraph",
+      "args": ["serve", "--mcp"]
+    }
+  }
+}
+`));
+                console.error('Available tools:');
+                console.error(chalk.cyan('  codegraph_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);
+        }
+    });
+    /**
+     * codegraph unlock [path]
+     */
+    program
+        .command('unlock [path]')
+        .description('Remove a stale lock file that is blocking indexing')
+        .action(async (pathArg) => {
+        const projectPath = resolveProjectPath(pathArg);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense not initialized in ${projectPath}`);
+                return;
+            }
+            const lockPath = path.join((0, directory_1.getAlphaCsDir)(projectPath), 'codegraph.lock');
+            let removed = false;
+            if (fs.existsSync(lockPath)) {
+                fs.unlinkSync(lockPath);
+                removed = true;
+            }
+            const { clearStaleDaemonArtifacts } = await Promise.resolve().then(() => __importStar(require('../mcp/daemon-registry')));
+            removed = await clearStaleDaemonArtifacts(projectPath) || removed;
+            if (removed)
+                success('Removed stale lock artifacts. You can now run indexing again.');
+            else
+                info(`No stale lock files found ${(0, glyphs_1.getGlyphs)().dash} nothing to do`);
+        }
+        catch (err) {
+            error(`Failed to remove lock: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * CLI parity with MCP callers/callees: resolve once, then collect and limit
+     * within each definition. The legacy JSON list remains an explicitly labeled
+     * union, with its original total/limit/truncated contract (#1674).
+     */
+    for (const direction of ['callers', 'callees']) {
+        const title = direction === 'callers' ? 'Callers' : 'Callees';
+        program
+            .command(`${direction} <symbol>`)
+            .description(direction === 'callers'
+            ? 'Find all functions/methods that call a specific symbol'
+            : 'Find all functions/methods called by a specific symbol')
+            .option('-p, --path <path>', 'Project path')
+            .option('-f, --file <path>', 'Narrow definitions by file path or suffix (no match: show all with a note)')
+            .option('-l, --limit <number>', 'Maximum results per definition (also caps the JSON union)', '20')
+            .option('-j, --json', 'Output as JSON')
+            .action(async (symbol, options) => {
+            const projectPath = resolveProjectPath(options.path);
+            try {
+                if (!(0, directory_1.isInitialized)(projectPath)) {
+                    error(`Alpha Code Sense not initialized in ${projectPath}`);
+                    process.exit(1);
+                }
+                const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+                const cg = await AlphaCodeSense.open(projectPath);
+                try {
+                    const limit = parseInt(options.limit || '20', 10);
+                    const { nodes: targets } = (0, symbol_lookup_1.lookupSymbolNodes)(cg, symbol);
+                    if (targets.length === 0) {
+                        info(formatSymbolNotFound(symbol, cg.searchNodes(symbol, { limit: 5 }).map((m) => m.node.name)));
+                        return;
+                    }
+                    const { groups, filteredOut } = (0, symbol_lookup_1.groupDefinitions)(targets, options.file);
+                    const ambiguous = groups.length > 1;
+                    const note = filteredOut
+                        ? `no definition of "${symbol}" matches file "${options.file}" — showing all definitions instead.`
+                        : undefined;
+                    const collected = groups.map((group) => {
+                        const nodes = new Map();
+                        const edges = new Map();
+                        for (const target of group) {
+                            const connections = direction === 'callers' ? cg.getCallers(target.id) : cg.getCallees(target.id);
+                            for (const { node, edge } of connections) {
+                                nodes.set(node.id, node);
+                                edges.set(`${edge.source}->${edge.target}:${edge.kind}`, edge);
+                            }
+                        }
+                        return { group, nodes: [...nodes.values()], edges: [...edges.values()] };
+                    });
+                    if (options.json) {
+                        const definitions = collected.map(({ group, nodes, edges }) => {
+                            const limited = nodes.slice(0, limit);
+                            const shown = new Set(limited.map((node) => node.id));
+                            return {
+                                ...cliDefinition(group),
+                                [direction]: limited.map((node) => ({ id: node.id, ...cliNode(node) })),
+                                edges: edges.filter((edge) => shown.has(direction === 'callers' ? edge.source : edge.target)),
+                                total: nodes.length,
+                                limit,
+                                truncated: nodes.length > limit,
+                            };
+                        });
+                        const union = new Map();
+                        for (const { nodes } of collected) {
+                            for (const node of nodes)
+                                union.set(node.id, node);
+                        }
+                        const total = union.size;
+                        console.log(JSON.stringify({
+                            symbol,
+                            targets: groups.flat().map((node) => cliDefinition([node]).definition),
+                            ambiguous,
+                            aggregation: ambiguous ? 'union' : 'definition',
+                            file: options.file,
+                            filteredOut,
+                            note,
+                            definitions,
+                            [direction]: [...union.values()].slice(0, limit).map(cliNode),
+                            total,
+                            limit,
+                            truncated: total > limit,
+                        }, null, 2));
+                    }
+                    else {
+                        if (note)
+                            warn(note);
+                        if (ambiguous) {
+                            console.log(chalk.bold(`\n${title} of "${symbol}" — ${groups.length} distinct definitions (narrow with --file):`));
+                        }
+                        for (const { group, nodes } of collected) {
+                            const limited = nodes.slice(0, limit);
+                            const total = nodes.length;
+                            const truncated = total > limit;
+                            const count = truncated ? `${limited.length} of ${total}` : String(total);
+                            if (ambiguous) {
+                                console.log(chalk.bold(`\n${(0, symbol_lookup_1.describeSymbolNode)(group[0])} (${count}):\n`));
+                            }
+                            else {
+                                console.log(chalk.bold(`\n${title} of "${symbol}" (${count}):\n`));
+                                console.log(chalk.dim((0, symbol_lookup_1.describeSymbolNode)(group[0])));
+                            }
+                            if (total === 0) {
+                                if (ambiguous)
+                                    console.log(chalk.dim(`  (no ${direction})`));
+                                else
+                                    info(`No ${direction} found for "${symbol}"`);
+                            }
+                            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();
+                            }
+                            if (truncated)
+                                console.log(chalk.dim(`Showing ${limited.length} of ${total}; pass --limit to widen.`));
+                        }
+                    }
+                }
+                finally {
+                    cg.destroy();
+                }
+            }
+            catch (err) {
+                error(`${direction} failed: ${err instanceof Error ? err.message : String(err)}`);
+                process.exit(1);
+            }
+        });
+    }
+    /**
+     * codegraph impact <symbol> — one blast radius per distinct definition.
+     */
+    program
+        .command('impact <symbol>')
+        .description('Analyze what code is affected by changing a symbol')
+        .option('-p, --path <path>', 'Project path')
+        .option('-f, --file <path>', 'Narrow definitions by file path or suffix (no match: show all with a note)')
+        .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(`Alpha Code Sense not initialized in ${projectPath}`);
+                process.exit(1);
+            }
+            const { default: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            try {
+                const depth = Math.min(Math.max(parseInt(options.depth || '2', 10), 1), 10);
+                const { nodes: targets } = (0, symbol_lookup_1.lookupSymbolNodes)(cg, symbol);
+                if (targets.length === 0) {
+                    info(formatSymbolNotFound(symbol, cg.searchNodes(symbol, { limit: 5 }).map((m) => m.node.name)));
+                    return;
+                }
+                const { groups, filteredOut } = (0, symbol_lookup_1.groupDefinitions)(targets, options.file);
+                const ambiguous = groups.length > 1;
+                const note = filteredOut
+                    ? `no definition of "${symbol}" matches file "${options.file}" — showing all definitions instead.`
+                    : undefined;
+                const collected = groups.map((group) => {
+                    const nodes = new Map();
+                    const edges = new Map();
+                    for (const target of group) {
+                        const impact = cg.getImpactRadius(target.id, depth);
+                        for (const [id, node] of impact.nodes)
+                            nodes.set(id, node);
+                        for (const edge of impact.edges)
+                            edges.set(`${edge.source}->${edge.target}:${edge.kind}`, edge);
+                    }
+                    return { group, nodes, edges };
+                });
+                if (options.json) {
+                    const unionNodes = new Map();
+                    const unionEdges = new Map();
+                    const definitions = collected.map(({ group, nodes, edges }) => {
+                        for (const [id, node] of nodes)
+                            unionNodes.set(id, node);
+                        for (const [key, edge] of edges)
+                            unionEdges.set(key, edge);
+                        return {
+                            ...cliDefinition(group),
+                            nodeCount: nodes.size,
+                            edgeCount: edges.size,
+                            affected: [...nodes.values()].map((node) => ({ id: node.id, ...cliNode(node) })),
+                            edges: [...edges.values()],
+                        };
+                    });
+                    console.log(JSON.stringify({
+                        symbol,
+                        depth,
+                        targets: groups.flat().map((node) => cliDefinition([node]).definition),
+                        ambiguous,
+                        aggregation: ambiguous ? 'union' : 'definition',
+                        file: options.file,
+                        filteredOut,
+                        note,
+                        definitions,
+                        nodeCount: unionNodes.size,
+                        edgeCount: unionEdges.size,
+                        affected: [...unionNodes.values()].map(cliNode),
+                    }, null, 2));
+                }
+                else {
+                    if (note)
+                        warn(note);
+                    if (ambiguous) {
+                        console.log(chalk.bold(`\nImpact of changing "${symbol}" — ${groups.length} distinct definitions (each with its own blast radius; narrow with --file):`));
+                    }
+                    for (const { group, nodes } of collected) {
+                        if (ambiguous) {
+                            console.log(chalk.bold(`\n${(0, symbol_lookup_1.describeSymbolNode)(group[0])} — ${nodes.size} affected symbols:\n`));
+                        }
+                        else {
+                            console.log(chalk.bold(`\nImpact of changing "${symbol}" — ${nodes.size} affected symbols:\n`));
+                            console.log(chalk.dim((0, symbol_lookup_1.describeSymbolNode)(group[0])));
+                        }
+                        const byFile = new Map();
+                        for (const node of nodes.values()) {
+                            const list = byFile.get(node.filePath) || [];
+                            list.push(node);
+                            byFile.set(node.filePath, list);
+                        }
+                        for (const [file, affected] of byFile) {
+                            console.log(chalk.cyan(file));
+                            for (const node of affected) {
+                                const loc = node.startLine ? `:${node.startLine}` : '';
+                                console.log(`  ${chalk.dim(node.kind.padEnd(12))}${node.name}${chalk.dim(loc)}`);
+                            }
+                            console.log();
+                        }
+                    }
+                }
+            }
+            finally {
+                cg.destroy();
+            }
+        }
+        catch (err) {
+            error(`impact failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph affected [files...]
+     *
+     * Find test files affected by the given source files.
+     * Traces dependency edges transitively to find test files that depend on changed code.
+     *
+     * Usage:
+     *   git diff --name-only | codegraph affected --stdin
+     *   codegraph affected src/lib/components/Editor.svelte src/routes/+page.svelte
+     */
+    program
+        .command('affected [files...]')
+        .description('Find test files affected by changed source files')
+        .option('-p, --path <path>', 'Project path')
+        .option('--stdin', 'Read file list from stdin (one per line)')
+        .option('-d, --depth <number>', 'Max dependency traversal depth', '5')
+        .option('-f, --filter <glob>', 'Custom glob filter for test files (e.g. "e2e/*.spec.ts")')
+        .option('-j, --json', 'Output as JSON')
+        .option('-q, --quiet', 'Only output file paths, no decoration')
+        .action(async (fileArgs, options) => {
+        const projectPath = resolveProjectPath(options.path);
+        try {
+            if (!(0, directory_1.isInitialized)(projectPath)) {
+                error(`Alpha Code Sense 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: AlphaCodeSense } = await loadAlphaCodeSense();
+            const cg = await AlphaCodeSense.open(projectPath);
+            const maxDepth = parseInt(options.depth || '5', 10);
+            // 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);
+            }
+            // One notion of "a test" for the whole tool (#1507): the CLI used to keep
+            // its own six regexes here, which knew `.test.` and `/tests/` but not Go's
+            // `_test.go`, Python's `test_x.py` or the JVM's `FooTest.kt` — so
+            // `affected` reported "no tests" for whole ecosystems while `search` and
+            // the MCP tools counted those very files as tests.
+            function isTestFile(filePath) {
+                if (customFilter)
+                    return customFilter.test(filePath);
+                return (0, query_utils_1.isTestPath)(filePath);
+            }
+            // BFS to find all transitive dependents of changed files, filtered to test files
+            const affectedTests = new Set();
+            const allDependents = new Set();
+            for (const file of changedFiles) {
+                // If the changed file is itself a test file, include it
+                if (isTestFile(file)) {
+                    affectedTests.add(file);
+                    continue;
+                }
+                // BFS through dependents
+                const queue = [{ file, depth: 0 }];
+                const visited = new Set();
+                visited.add(file);
+                while (queue.length > 0) {
+                    const current = queue.shift();
+                    if (current.depth >= maxDepth)
+                        continue;
+                    const dependents = cg.getFileDependents(current.file);
+                    for (const dep of dependents) {
+                        if (visited.has(dep))
+                            continue;
+                        visited.add(dep);
+                        allDependents.add(dep);
+                        if (isTestFile(dep)) {
+                            affectedTests.add(dep);
+                        }
+                        else {
+                            queue.push({ file: dep, depth: current.depth + 1 });
+                        }
+                    }
+                }
+            }
+            const sortedTests = Array.from(affectedTests).sort();
+            // Output
+            if (options.json) {
+                console.log(JSON.stringify({
+                    changedFiles,
+                    affectedTests: sortedTests,
+                    totalDependentsTraversed: allDependents.size,
+                }, null, 2));
+            }
+            else if (options.quiet) {
+                for (const t of sortedTests)
+                    console.log(t);
+            }
+            else {
+                if (sortedTests.length === 0) {
+                    info('No test files affected by the changed files.');
+                }
+                else {
+                    console.log(chalk.bold(`\nAffected test files (${sortedTests.length}):\n`));
+                    for (const t of sortedTests) {
+                        console.log('  ' + chalk.cyan(t));
+                    }
+                    console.log();
+                }
+            }
+            cg.destroy();
+        }
+        catch (err) {
+            error(`Affected analysis failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph install
+     */
+    program
+        .command('install')
+        .description('Install codegraph MCP server into one or more agents (Claude Code, Cursor, Codex CLI, opencode, Hermes Agent, Gemini CLI, Antigravity IDE, Kiro, GitHub Copilot)')
+        .option('-t, --target <ids>', 'Target agent(s): comma-separated ids, or "auto"|"all"|"none". Default: prompt')
+        .option('-l, --location <where>', 'Install location: "global" or "local". Default: prompt')
+        .option('-y, --yes', 'Non-interactive: defaults to --location=global --target=auto, auto-allow on')
+        .option('-i, --init', 'After wiring agents, also run `codegraph init` in the current directory — builds this project’s index, so install + index is one command (combine with --yes for an unattended bootstrap)')
+        .option('--no-permissions', 'Skip writing the auto-allow permissions list (Claude Code only)')
+        .option('--print-config <id>', 'Print MCP config snippet for the named agent and exit (no file writes)')
+        .option('--refresh', 'Rewrite what previous installs configured, for already-configured agents only (never adds new ones). Run automatically by `ltm-alpha-cs upgrade`')
+        .action(async (opts) => {
+        if (opts.printConfig) {
+            const { getTarget, listTargetIds } = await Promise.resolve().then(() => __importStar(require('../installer/targets/registry')));
+            const target = getTarget(opts.printConfig);
+            if (!target) {
+                const known = listTargetIds().join(', ');
+                error(`Unknown target "${opts.printConfig}". Known: ${known}.`);
+                process.exit(1);
+            }
+            const loc = (opts.location === 'local' ? 'local' : 'global');
+            process.stdout.write(target.printConfig(loc));
+            return;
+        }
+        // --refresh: non-interactive sweep that re-writes what previous
+        // installs configured (instructions section, MCP entry, legacy-hook
+        // cleanups) for already-configured agents, so those surfaces match
+        // THIS binary's templates. Skips everything else — never a first
+        // install, never touches permissions or the prompt hook. Sweeps both
+        // locations unless --location narrows it.
+        if (opts.refresh) {
+            const { refreshTargets } = await Promise.resolve().then(() => __importStar(require('../installer')));
+            const { ALL_TARGETS } = await Promise.resolve().then(() => __importStar(require('../installer/targets/registry')));
+            if (opts.location && opts.location !== 'global' && opts.location !== 'local') {
+                error(`--location must be "global" or "local" (got "${opts.location}").`);
+                process.exit(1);
+            }
+            const locs = opts.location
+                ? [opts.location]
+                : ['global', 'local'];
+            let changed = 0;
+            for (const loc of locs) {
+                for (const report of refreshTargets(ALL_TARGETS, loc)) {
+                    for (const p of report.changedPaths) {
+                        changed += 1;
+                        console.log(`  ${report.displayName}: refreshed ${p}`);
+                    }
+                }
+            }
+            if (changed === 0) {
+                console.log('All configured agent surfaces are already current.');
+            }
+            return;
+        }
+        const { runInstallerWithOptions } = await Promise.resolve().then(() => __importStar(require('../installer')));
+        if (opts.location && opts.location !== 'global' && opts.location !== 'local') {
+            error(`--location must be "global" or "local" (got "${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);
+        }
+        // --init: the one-shot "wire agents AND build this project's index"
+        // bootstrap (#1578). The installer itself never indexes implicitly (a
+        // surprise index of $HOME is the thing we refuse) — an explicit flag is
+        // the user choosing. Runs after a successful install, including the
+        // `--target none` / nothing-detected case (the installer returns normally
+        // there), and shares every guard with `codegraph init`: an unsafe root
+        // is refused (exit 1, no implied --force), an already-initialized
+        // project just says so. `--yes` flows through so no offer prompts.
+        if (opts.init) {
+            await runInit(process.cwd(), { yes: opts.yes });
+        }
+    });
+    /**
+     * ltm-alpha-cs uninstall
+     *
+     * Inverse of `install`. Removes the codegraph MCP server entry,
+     * instructions block, and permissions from every agent (or a
+     * `--target` subset). Prompts global-vs-local when not given. Does NOT
+     * delete the `.alpha-cs/` index — that's `codegraph uninit`.
+     */
+    program
+        .command('uninstall')
+        .description('Remove codegraph from your agents (Claude Code, Cursor, Codex CLI, opencode, Hermes Agent, Gemini CLI, Antigravity IDE, Kiro, GitHub Copilot)')
+        .option('-t, --target <ids>', 'Target agent(s): comma-separated ids, or "all". Default: all')
+        .option('-l, --location <where>', 'Uninstall location: "global" or "local". Default: prompt')
+        .option('-y, --yes', 'Non-interactive: defaults to --location=global --target=all')
+        .option('--keep-cli', 'Remove agent configs only — leave the codegraph CLI installed')
+        .action(async (opts) => {
+        const { runUninstaller } = await Promise.resolve().then(() => __importStar(require('../installer')));
+        if (opts.location && opts.location !== 'global' && opts.location !== 'local') {
+            error(`--location must be "global" or "local" (got "${opts.location}").`);
+            process.exit(1);
+        }
+        try {
+            await runUninstaller({
+                target: opts.target,
+                location: opts.location,
+                yes: opts.yes,
+                keepCli: opts.keepCli,
+                cliFilename: __filename,
+            });
+        }
+        catch (err) {
+            error(err instanceof Error ? err.message : String(err));
+            process.exit(1);
+        }
+    });
+    /**
+     * codegraph 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 === 'CODEGRAPH_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',
+            CODEGRAPH_TELEMETRY: 'CODEGRAPH_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`));
+    });
+    /**
+     * ltm-alpha-cs upgrade [version]
+     *
+     * Self-update, however Alpha Code Sense 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 Alpha Code Sense 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.CODEGRAPH_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,
+            capture: up.defaultCapture,
+            hasCommand: up.hasCommand,
+            log: (m) => console.log(m),
+            warn: (m) => warn(m),
+            error: (m) => error(m),
+            platform: process.platform,
+        });
+        process.exit(code);
+    });
+    /**
+     * codegraph 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 `codegraph version` work and lists
+     * the version affordance in `codegraph --help`.
+     */
+    program
+        .command('version')
+        .description('Print the installed Alpha Code Sense version (also: -v, --version)')
+        .action(() => {
+        console.log(packageJson.version);
+    });
+    // Parse and run
+    program.parse();
+} // end main()
+//# sourceMappingURL=ltm-alpha-cs.js.map