cgraphx 1.4.3 → 2.0.0

package/dist/utils.js

@@ -1,583 +0,0 @@
-"use strict";
-/**
- * CodeGraph Utilities
- *
- * Common utility functions for memory management, concurrency, batching,
- * and security validation.
- *
- * @module utils
- *
- * @example
- * ```typescript
- * import { Mutex, processInBatches, MemoryMonitor, validatePathWithinRoot } from 'cgraphx';
- *
- * // Use mutex for concurrent safety
- * const mutex = new Mutex();
- * await mutex.withLock(async () => {
- *   await performCriticalOperation();
- * });
- *
- * // Process items in batches to manage memory
- * const results = await processInBatches(items, 100, async (item) => {
- *   return await processItem(item);
- * });
- *
- * // Monitor memory usage
- * const monitor = new MemoryMonitor(512, (usage) => {
- *   console.warn(`Memory usage exceeded 512MB: ${usage / 1024 / 1024}MB`);
- * });
- * monitor.start();
- * ```
- */
-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 });
-exports.MemoryMonitor = exports.Mutex = exports.FileLock = exports.CONFIG_LEAF_LANGUAGES = void 0;
-exports.isConfigLeafNode = isConfigLeafNode;
-exports.validatePathWithinRoot = validatePathWithinRoot;
-exports.validateProjectPath = validateProjectPath;
-exports.safeJsonParse = safeJsonParse;
-exports.clamp = clamp;
-exports.normalizePath = normalizePath;
-exports.processInBatches = processInBatches;
-exports.readFileInChunks = readFileInChunks;
-exports.debounce = debounce;
-exports.throttle = throttle;
-exports.estimateSize = estimateSize;
-const fs = __importStar(require("fs"));
-const path = __importStar(require("path"));
-// ============================================================
-// SECURITY UTILITIES
-// ============================================================
-/**
- * Sensitive system directories that should never be used as project roots.
- * Checked on all platforms; non-applicable paths are harmlessly skipped.
- */
-const SENSITIVE_PATHS = new Set([
-    '/', '/etc', '/usr', '/bin', '/sbin', '/var', '/tmp', '/dev', '/proc', '/sys',
-    '/root', '/boot', '/lib', '/lib64', '/opt',
-    'c:\\', 'c:\\windows', 'c:\\windows\\system32',
-]);
-/**
- * Config "languages" whose nodes are pure key/value DATA lifted from a config
- * file (e.g. Spring `application.{yml,properties}`), not source code.
- */
-exports.CONFIG_LEAF_LANGUAGES = new Set(['yaml', 'properties']);
-/**
- * A config-leaf node is a single key lifted out of a pure config/data file —
- * `kind: 'constant'` in a {@link CONFIG_LEAF_LANGUAGES} language. Its on-disk
- * line is `key = <value>`, and that value is routinely a secret (DB password,
- * API key, JDBC URL with embedded creds). CodeGraph must surface the KEY only
- * and never read/return the value, or it pushes secrets into agent context
- * unbidden — the value isn't needed for resolution, and an agent that genuinely
- * needs it can read the file directly. (#383)
- */
-function isConfigLeafNode(node) {
-    return node.kind === 'constant' && !!node.language && exports.CONFIG_LEAF_LANGUAGES.has(node.language);
-}
-/**
- * Whether `child` is `parent` itself or sits underneath it. Case-insensitive on
- * Windows — NTFS is case-insensitive, and realpathSync can hand back a different
- * case than the lexical root, which would otherwise false-reject a valid file.
- */
-function isWithinDir(child, parent) {
-    let c = child;
-    let p = parent;
-    if (process.platform === 'win32') {
-        c = c.toLowerCase();
-        p = p.toLowerCase();
-    }
-    return c === p || c.startsWith(p + path.sep);
-}
-/**
- * Validate that a file path stays within the project root, resolving symlinks.
- *
- * Two layers: a cheap lexical check that catches `../` traversal, then a
- * realpath check that catches symlink escapes — an in-repo symlink whose
- * logical path is inside the root but whose real target points outside it
- * (issue #527). A symlink that stays within the root is still allowed, so
- * legitimate in-tree symlinks keep working. Both content-serving read sinks
- * (codegraph_node `includeCode`, codegraph_explore source) go through here, so
- * this is the chokepoint that keeps out-of-root file contents from leaking.
- *
- * `allowSymlinkEscape` waives **only** the realpath-escape rejection (the
- * lexical `../` guard still applies) for the INDEXING read path. The directory
- * walk deliberately descends into in-root symlinks whose targets live outside
- * the root (e.g. a `game/` symlink in a Dota custom-game tree, #935); discovery
- * and the reader must agree, or every file the walk enumerated fails to index.
- * Indexing only reads paths it just discovered, into a local index — it never
- * serves them to an agent, so this does not widen the #527 leak surface. The
- * content-serving sinks must never pass this flag.
- *
- * @param projectRoot - The project root directory
- * @param filePath - The (relative or absolute) file path to validate
- * @param options.allowSymlinkEscape - Follow in-root symlinks out of the root
- *   (indexing read path only); defaults to the strict, leak-safe behavior.
- * @returns The resolved absolute path (realpath when it exists), or null if it
- *   escapes the root
- */
-function validatePathWithinRoot(projectRoot, filePath, options) {
-    const resolved = path.resolve(projectRoot, filePath);
-    const normalizedRoot = path.resolve(projectRoot);
-    // 1. Lexical containment — cheap, catches `../` traversal. Applies even on
-    //    the indexing read path: a crafted `../` escape is still rejected.
-    if (!isWithinDir(resolved, normalizedRoot)) {
-        return null;
-    }
-    // 2. Symlink-aware containment — resolve symlinks on both sides and re-check,
-    //    so an in-repo symlink whose real target escapes the root is rejected.
-    //    The indexing read path (allowSymlinkEscape) skips only this rejection so
-    //    it stays consistent with the directory walk, which already followed the
-    //    in-root symlink to enumerate these files (#935).
-    try {
-        const realRoot = fs.realpathSync(normalizedRoot);
-        const realResolved = fs.realpathSync(resolved);
-        if (options?.allowSymlinkEscape) {
-            return realResolved;
-        }
-        return isWithinDir(realResolved, realRoot) ? realResolved : null;
-    }
-    catch (err) {
-        // ENOENT: the path doesn't exist yet (a file about to be written, or an
-        // index entry for a since-deleted file) — no symlink to follow, and the
-        // lexical check already passed, so allow the lexical path. Any other
-        // resolution failure (ELOOP, EACCES, …) is treated as unsafe → reject.
-        if (err.code === 'ENOENT') {
-            return resolved;
-        }
-        return null;
-    }
-}
-/**
- * Validate that a path is a safe project root directory.
- *
- * Rejects sensitive system directories and ensures the path is
- * a real, existing directory. Used at MCP and API entry points
- * to prevent arbitrary directory access.
- *
- * @param dirPath - The path to validate
- * @returns An error message if invalid, or null if valid
- */
-function validateProjectPath(dirPath) {
-    const resolved = path.resolve(dirPath);
-    // Block sensitive system directories
-    if (SENSITIVE_PATHS.has(resolved) || SENSITIVE_PATHS.has(resolved.toLowerCase())) {
-        return `Refusing to operate on sensitive system directory: ${resolved}`;
-    }
-    // Also block common sensitive home subdirectories
-    const homeDir = require('os').homedir();
-    const sensitiveHomeDirs = ['.ssh', '.gnupg', '.aws', '.config'];
-    for (const dir of sensitiveHomeDirs) {
-        const sensitivePath = path.join(homeDir, dir);
-        if (resolved === sensitivePath || resolved.startsWith(sensitivePath + path.sep)) {
-            return `Refusing to operate on sensitive directory: ${resolved}`;
-        }
-    }
-    // Verify it's a real directory
-    try {
-        const stats = fs.statSync(resolved);
-        if (!stats.isDirectory()) {
-            return `Path is not a directory: ${resolved}`;
-        }
-    }
-    catch {
-        return `Path does not exist or is not accessible: ${resolved}`;
-    }
-    return null;
-}
-/**
- * Safely parse JSON with a fallback value.
- * Prevents crashes from corrupted database metadata.
- */
-function safeJsonParse(value, fallback) {
-    try {
-        return JSON.parse(value);
-    }
-    catch {
-        return fallback;
-    }
-}
-/**
- * Clamp a numeric value to a range.
- * Used to enforce sane limits on MCP tool inputs.
- */
-function clamp(value, min, max) {
-    return Math.max(min, Math.min(max, value));
-}
-/**
- * Normalize a file path to use forward slashes.
- * Fixes Windows backslash paths so glob matching works consistently.
- */
-function normalizePath(filePath) {
-    return filePath.replace(/\\/g, '/');
-}
-/**
- * Cross-process file lock using a lock file with PID tracking.
- *
- * Prevents multiple processes (e.g., git hooks, CLI, MCP server) from
- * writing to the same database simultaneously.
- */
-class FileLock {
-    lockPath;
-    held = false;
-    /** Locks older than this are considered stale regardless of PID status */
-    static STALE_TIMEOUT_MS = 2 * 60 * 1000; // 2 minutes
-    constructor(lockPath) {
-        this.lockPath = lockPath;
-    }
-    /**
-     * Acquire the lock. Throws if the lock is held by another live process.
-     */
-    acquire() {
-        // Check for existing lock
-        if (fs.existsSync(this.lockPath)) {
-            try {
-                const content = fs.readFileSync(this.lockPath, 'utf-8').trim();
-                const pid = parseInt(content, 10);
-                const stat = fs.statSync(this.lockPath);
-                const lockAge = Date.now() - stat.mtimeMs;
-                // Treat locks older than the timeout as stale, regardless of PID
-                if (lockAge < FileLock.STALE_TIMEOUT_MS && !isNaN(pid) && this.isProcessAlive(pid)) {
-                    throw new Error(`cgraphx database is locked by another process (PID ${pid}). ` +
-                        `If this is stale, run 'cgraphx unlock' or delete ${this.lockPath}`);
-                }
-                // Stale lock (dead process or timed out) - remove it
-                fs.unlinkSync(this.lockPath);
-            }
-            catch (err) {
-                if (err instanceof Error && err.message.includes('locked by another')) {
-                    throw err;
-                }
-                // Other errors reading lock file - try to remove it
-                try {
-                    fs.unlinkSync(this.lockPath);
-                }
-                catch { /* ignore */ }
-            }
-        }
-        // Write our PID to the lock file using exclusive create flag
-        try {
-            fs.writeFileSync(this.lockPath, String(process.pid), { flag: 'wx' });
-            this.held = true;
-        }
-        catch (err) {
-            if (err.code === 'EEXIST') {
-                // Race condition: another process grabbed the lock between our check and write
-                throw new Error('cgraphx database is locked by another process. ' +
-                    `If this is stale, run 'cgraphx unlock' or delete ${this.lockPath}`);
-            }
-            throw err;
-        }
-    }
-    /**
-     * Release the lock
-     */
-    release() {
-        if (!this.held)
-            return;
-        try {
-            // Only remove if we still own it (check PID)
-            const content = fs.readFileSync(this.lockPath, 'utf-8').trim();
-            if (parseInt(content, 10) === process.pid) {
-                fs.unlinkSync(this.lockPath);
-            }
-        }
-        catch {
-            // Lock file already gone - that's fine
-        }
-        this.held = false;
-    }
-    /**
-     * Execute a function while holding the lock
-     */
-    withLock(fn) {
-        this.acquire();
-        try {
-            return fn();
-        }
-        finally {
-            this.release();
-        }
-    }
-    /**
-     * Execute an async function while holding the lock
-     */
-    async withLockAsync(fn) {
-        this.acquire();
-        try {
-            return await fn();
-        }
-        finally {
-            this.release();
-        }
-    }
-    /**
-     * Check if a process is still running
-     */
-    isProcessAlive(pid) {
-        try {
-            process.kill(pid, 0);
-            return true;
-        }
-        catch {
-            return false;
-        }
-    }
-}
-exports.FileLock = FileLock;
-/**
- * Process items in batches to manage memory
- *
- * @param items - Array of items to process
- * @param batchSize - Number of items per batch
- * @param processor - Function to process each item
- * @param onBatchComplete - Optional callback after each batch
- * @returns Array of results
- */
-async function processInBatches(items, batchSize, processor, onBatchComplete) {
-    const results = [];
-    for (let i = 0; i < items.length; i += batchSize) {
-        const batch = items.slice(i, Math.min(i + batchSize, items.length));
-        const batchResults = await Promise.all(batch.map((item, idx) => processor(item, i + idx)));
-        results.push(...batchResults);
-        if (onBatchComplete) {
-            onBatchComplete(Math.min(i + batchSize, items.length), items.length);
-        }
-        // Allow GC between batches
-        if (global.gc) {
-            global.gc();
-        }
-    }
-    return results;
-}
-/**
- * Simple mutex lock for preventing concurrent operations
- */
-class Mutex {
-    locked = false;
-    waitQueue = [];
-    /**
-     * Acquire the lock
-     *
-     * @returns A release function to call when done
-     */
-    async acquire() {
-        while (this.locked) {
-            await new Promise((resolve) => {
-                this.waitQueue.push(resolve);
-            });
-        }
-        this.locked = true;
-        return () => {
-            this.locked = false;
-            const next = this.waitQueue.shift();
-            if (next) {
-                next();
-            }
-        };
-    }
-    /**
-     * Execute a function while holding the lock
-     */
-    async withLock(fn) {
-        const release = await this.acquire();
-        try {
-            return await fn();
-        }
-        finally {
-            release();
-        }
-    }
-    /**
-     * Check if the lock is currently held
-     */
-    isLocked() {
-        return this.locked;
-    }
-}
-exports.Mutex = Mutex;
-/**
- * Chunked file reader for large files
- *
- * Reads a file in chunks to avoid loading entire file into memory.
- */
-async function* readFileInChunks(filePath, chunkSize = 64 * 1024) {
-    const fs = await Promise.resolve().then(() => __importStar(require('fs')));
-    const fd = fs.openSync(filePath, 'r');
-    const buffer = Buffer.alloc(chunkSize);
-    try {
-        let bytesRead;
-        while ((bytesRead = fs.readSync(fd, buffer, 0, chunkSize, null)) > 0) {
-            yield buffer.toString('utf-8', 0, bytesRead);
-        }
-    }
-    finally {
-        fs.closeSync(fd);
-    }
-}
-/**
- * Debounce a function
- *
- * @param fn - Function to debounce
- * @param delay - Delay in milliseconds
- * @returns Debounced function
- */
-function debounce(fn, delay) {
-    let timeoutId = null;
-    return (...args) => {
-        if (timeoutId) {
-            clearTimeout(timeoutId);
-        }
-        timeoutId = setTimeout(() => {
-            fn(...args);
-            timeoutId = null;
-        }, delay);
-    };
-}
-/**
- * Throttle a function
- *
- * @param fn - Function to throttle
- * @param limit - Minimum time between calls in milliseconds
- * @returns Throttled function
- */
-function throttle(fn, limit) {
-    let lastCall = 0;
-    let timeoutId = null;
-    return (...args) => {
-        const now = Date.now();
-        const remaining = limit - (now - lastCall);
-        if (remaining <= 0) {
-            if (timeoutId) {
-                clearTimeout(timeoutId);
-                timeoutId = null;
-            }
-            lastCall = now;
-            fn(...args);
-        }
-        else if (!timeoutId) {
-            timeoutId = setTimeout(() => {
-                lastCall = Date.now();
-                timeoutId = null;
-                fn(...args);
-            }, remaining);
-        }
-    };
-}
-/**
- * Estimate memory usage of an object (rough approximation)
- *
- * @param obj - Object to measure
- * @returns Approximate size in bytes
- */
-function estimateSize(obj) {
-    const seen = new WeakSet();
-    function sizeOf(value) {
-        if (value === null || value === undefined) {
-            return 0;
-        }
-        switch (typeof value) {
-            case 'boolean':
-                return 4;
-            case 'number':
-                return 8;
-            case 'string':
-                return 2 * value.length;
-            case 'object':
-                if (seen.has(value)) {
-                    return 0;
-                }
-                seen.add(value);
-                if (Array.isArray(value)) {
-                    return value.reduce((acc, item) => acc + sizeOf(item), 0);
-                }
-                return Object.entries(value).reduce((acc, [key, val]) => acc + sizeOf(key) + sizeOf(val), 0);
-            default:
-                return 0;
-        }
-    }
-    return sizeOf(obj);
-}
-/**
- * Memory monitor for tracking usage during operations
- */
-class MemoryMonitor {
-    checkInterval = null;
-    peakUsage = 0;
-    threshold;
-    onThresholdExceeded;
-    constructor(thresholdMB = 500, onThresholdExceeded) {
-        this.threshold = thresholdMB * 1024 * 1024;
-        this.onThresholdExceeded = onThresholdExceeded;
-    }
-    /**
-     * Start monitoring memory usage
-     */
-    start(intervalMs = 1000) {
-        this.stop();
-        this.peakUsage = 0;
-        this.checkInterval = setInterval(() => {
-            const usage = process.memoryUsage().heapUsed;
-            if (usage > this.peakUsage) {
-                this.peakUsage = usage;
-            }
-            if (usage > this.threshold && this.onThresholdExceeded) {
-                this.onThresholdExceeded(usage);
-            }
-        }, intervalMs);
-    }
-    /**
-     * Stop monitoring
-     */
-    stop() {
-        if (this.checkInterval) {
-            clearInterval(this.checkInterval);
-            this.checkInterval = null;
-        }
-    }
-    /**
-     * Get peak memory usage in bytes
-     */
-    getPeakUsage() {
-        return this.peakUsage;
-    }
-    /**
-     * Get current memory usage in bytes
-     */
-    getCurrentUsage() {
-        return process.memoryUsage().heapUsed;
-    }
-}
-exports.MemoryMonitor = MemoryMonitor;
-//# sourceMappingURL=utils.js.map

package/dist/utils.js.map

@@ -1 +0,0 @@
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package/scripts/add-lang/bench.sh

@@ -1,60 +0,0 @@
-#!/usr/bin/env bash
-# Add-lang benchmark for ONE repo:
-#   clone -> wipe+index (with the codegraph on PATH) -> verify extraction ->
-#   with/without retrieval A/B (reuses scripts/agent-eval/run-all.sh).
-#
-# Assumes the codegraph dev build is already built + linked on PATH — the skill
-# runs `npm run build && ./scripts/local-install.sh` ONCE before looping repos.
-# The A/B is skipped if extraction fails its critical checks (don't burn $ on a
-# broken extractor); set FORCE_AB=1 to run it anyway.
-#
-# Usage: bench.sh <lang> <repo-name> <repo-url> "<question>" [headless|tmux|all]
-# Env:   CORPUS   corpus dir (default /tmp/codegraph-corpus, shared with agent-eval)
-set -uo pipefail
-
-LANG_TOKEN="${1:?usage: bench.sh <lang> <repo-name> <repo-url> \"<question>\" [mode]}"
-NAME="${2:?repo-name required}"
-URL="${3:?repo-url required}"
-Q="${4:?question required}"
-MODE="${5:-headless}"
-
-HARNESS="$(cd "$(dirname "$0")" && pwd)"
-AGENT_EVAL="$(cd "$HARNESS/../agent-eval" && pwd)"
-CORPUS="${CORPUS:-/tmp/codegraph-corpus}"
-REPO="$CORPUS/$NAME"
-
-command -v codegraph >/dev/null || { echo "no codegraph on PATH (build + ./scripts/local-install.sh first)"; exit 1; }
-
-echo "==================== add-lang bench: $NAME ($LANG_TOKEN) ===================="
-echo "codegraph: $(command -v codegraph) -> $(codegraph --version 2>/dev/null || echo '?')"
-
-# 1. Ensure the repo (shallow clone, reuse if present).
-mkdir -p "$CORPUS"
-if [ -d "$REPO/.git" ]; then
-  echo "→ reusing checkout: $REPO"
-else
-  echo "→ cloning $URL"
-  git clone --depth 1 "$URL" "$REPO" || { echo "git clone failed"; exit 1; }
-fi
-
-# 2. Wipe + index with the binary under test.
-echo "→ wiping .cgraphx and indexing"
-rm -rf "$REPO/.cgraphx"
-( cd "$REPO" && codegraph init -i ) || { echo "indexing failed"; exit 1; }
-
-# 3. Verify extraction (cheap guard before the paid A/B).
-echo "→ verifying extraction"
-node "$HARNESS/verify-extraction.mjs" "$REPO" "$LANG_TOKEN"
-VERIFY=$?
-
-# 4. Retrieval A/B (skipped if extraction is broken, unless FORCE_AB=1).
-if [ "$VERIFY" -ne 0 ] && [ "${FORCE_AB:-0}" != "1" ]; then
-  echo "→ SKIPPING A/B — extraction failed critical checks (set FORCE_AB=1 to override)"
-else
-  echo "→ retrieval A/B (mode=$MODE)"
-  bash "$AGENT_EVAL/run-all.sh" "$REPO" "$Q" "$MODE"
-fi
-
-echo "==================== bench complete: $NAME (verify exit=$VERIFY) ===================="
-# Exit reflects extraction: 0 = pass/warn, 1 = critical fail, 2 = couldn't read status.
-exit "$VERIFY"