@colbymchenry/codegraph 0.8.0 → 0.9.1

package/dist/utils.js

@@ -1,549 +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 'codegraph';
- *
- * // 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 = void 0;
-exports.validatePathWithinRoot = validatePathWithinRoot;
-exports.validateProjectPath = validateProjectPath;
-exports.isPathWithinRoot = isPathWithinRoot;
-exports.isPathWithinRootReal = isPathWithinRootReal;
-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',
-]);
-/**
- * Validate that a resolved file path stays within the project root.
- * Prevents path traversal attacks (e.g. node.filePath = "../../etc/passwd").
- *
- * @param projectRoot - The project root directory
- * @param filePath - The relative file path to validate
- * @returns The resolved absolute path, or null if it escapes the root
- */
-function validatePathWithinRoot(projectRoot, filePath) {
-    const resolved = path.resolve(projectRoot, filePath);
-    const normalizedRoot = path.resolve(projectRoot);
-    if (!resolved.startsWith(normalizedRoot + path.sep) && resolved !== normalizedRoot) {
-        return null;
-    }
-    return resolved;
-}
-/**
- * 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;
-}
-/**
- * Check if a file path resolves to a location within the given root directory.
- *
- * Prevents path traversal attacks by ensuring the resolved absolute path
- * starts with the resolved root path. Handles '..' sequences, symlink-like
- * relative paths, and platform-specific separators.
- *
- * @param filePath - The path to check (can be relative or absolute)
- * @param rootDir - The root directory that filePath must stay within
- * @returns true if filePath resolves to a location within rootDir
- */
-function isPathWithinRoot(filePath, rootDir) {
-    const resolvedPath = path.resolve(rootDir, filePath);
-    const resolvedRoot = path.resolve(rootDir);
-    return resolvedPath.startsWith(resolvedRoot + path.sep) || resolvedPath === resolvedRoot;
-}
-/**
- * Like isPathWithinRoot but also resolves symlinks via fs.realpathSync.
- *
- * This catches symlink escapes where the logical path appears to be within
- * root but the real path on disk points elsewhere. Falls back to logical
- * path checking if realpath resolution fails (e.g. broken symlink).
- */
-function isPathWithinRootReal(filePath, rootDir) {
-    // First do the cheap logical check
-    if (!isPathWithinRoot(filePath, rootDir)) {
-        return false;
-    }
-    // Then verify with realpath to catch symlink escapes
-    try {
-        const realPath = fs.realpathSync(path.resolve(rootDir, filePath));
-        const realRoot = fs.realpathSync(rootDir);
-        return realPath.startsWith(realRoot + path.sep) || realPath === realRoot;
-    }
-    catch {
-        // If realpath fails (broken symlink, permissions), fall back to logical check
-        return true;
-    }
-}
-/**
- * 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(`CodeGraph database is locked by another process (PID ${pid}). ` +
-                        `If this is stale, run 'codegraph 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('CodeGraph database is locked by another process. ' +
-                    `If this is stale, run 'codegraph 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/agent-eval/audit.sh

@@ -1,68 +0,0 @@
-#!/usr/bin/env bash
-# One-shot CodeGraph quality audit:
-#   set version -> ensure corpus repo -> wipe+reindex with that version ->
-#   run with/without A/B -> restore the local dev link.
-#
-# Usage: audit.sh <version> <repo-name> <repo-url> "<question>" [headless|all]
-#   <version>    "local" (build + npm link this repo) | "latest" | a version (e.g. 0.7.10)
-#   <repo-name>  dir name under the corpus dir
-#   <repo-url>   git URL (cloned --depth 1 when the repo dir is missing)
-#   [mode]       headless (default) | all (also the interactive tmux arms)
-# Env: CORPUS  corpus dir (default: /tmp/codegraph-corpus)
-set -uo pipefail
-
-VERSION="${1:?usage: audit.sh <version> <repo-name> <repo-url> \"<question>\" [mode]}"
-NAME="${2:?repo-name required}"
-URL="${3:?repo-url required}"
-Q="${4:?question required}"
-MODE="${5:-headless}"
-
-HARNESS="$(cd "$(dirname "$0")" && pwd)"
-REPO_ROOT="$(cd "$HARNESS/../.." && pwd)"     # codegraph repo root
-CORPUS="${CORPUS:-/tmp/codegraph-corpus}"
-REPO="$CORPUS/$NAME"
-PKG="@colbymchenry/codegraph"
-
-echo "==================== CodeGraph audit ===================="
-echo "version=$VERSION  repo=$NAME  mode=$MODE  corpus=$CORPUS"
-echo
-
-# 1. Set the codegraph version under test (mutates the global install).
-if [ "$VERSION" = local ]; then
-  echo "→ [1/4] building + linking local dev build (local-install.sh)"
-  ( cd "$REPO_ROOT" && ./scripts/local-install.sh ) || { echo "local-install.sh failed"; exit 1; }
-else
-  echo "→ [1/4] installing $PKG@$VERSION globally"
-  npm install -g "$PKG@$VERSION" || { echo "npm install -g $PKG@$VERSION failed"; exit 1; }
-fi
-ACTUAL="$(codegraph --version 2>/dev/null || echo '?')"
-echo "  codegraph on PATH: $(command -v codegraph) -> $ACTUAL"
-
-# 2. Ensure the corpus repo exists (clone shallow if missing, reuse if present).
-mkdir -p "$CORPUS"
-if [ -d "$REPO/.git" ]; then
-  echo "→ [2/4] reusing existing checkout: $REPO"
-else
-  echo "→ [2/4] cloning $URL"
-  git clone --depth 1 "$URL" "$REPO" || { echo "git clone failed"; exit 1; }
-fi
-
-# 3. Wipe + re-index with THIS version (the index must be built by the same
-#    binary that serves it — different versions extract differently).
-echo "→ [3/4] wiping .codegraph and re-indexing with $ACTUAL"
-rm -rf "$REPO/.codegraph"
-( cd "$REPO" && codegraph init -i ) || { echo "indexing failed"; exit 1; }
-
-# 4. Run the with/without A/B.
-echo "→ [4/4] running A/B harness (mode=$MODE)"
-bash "$HARNESS/run-all.sh" "$REPO" "$Q" "$MODE"
-
-# Restore the dev link (the normal working state in this repo).
-echo
-echo "→ restoring local dev link (local-install.sh)"
-if ( cd "$REPO_ROOT" && ./scripts/local-install.sh >/dev/null 2>&1 ); then
-  echo "  global codegraph restored to dev build"
-else
-  echo "  WARN: restore failed — run ./scripts/local-install.sh manually"
-fi
-echo "==================== audit complete ===================="