cgraphx 1.1.0

package/dist/utils.js

@@ -0,0 +1,583 @@
+"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

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,60 @@
+{
+  "name": "cgraphx",
+  "version": "1.1.0",
+  "description": "Supercharge AI coding agents with semantic code intelligence — surgical context, fewer tool calls, faster answers. 100% local.",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "cgraphx": "./dist/bin/codegraph.js"
+  },
+  "files": [
+    "dist",
+    "scripts",
+    "README.md"
+  ],
+  "scripts": {
+    "build": "tsc && npm run copy-assets && node -e \"require('fs').chmodSync('dist/bin/codegraph.js', 0o755)\"",
+    "preuninstall": "node dist/bin/uninstall.js",
+    "copy-assets": "node -e \"const fs=require('fs');const path=require('path');fs.mkdirSync('dist/db',{recursive:true});fs.copyFileSync('src/db/schema.sql','dist/db/schema.sql');fs.mkdirSync('dist/markdown',{recursive:true});fs.copyFileSync('src/markdown/schema.sql','dist/markdown/schema.sql');fs.mkdirSync('dist/timeline',{recursive:true});fs.copyFileSync('src/timeline/schema.sql','dist/timeline/schema.sql');fs.mkdirSync('dist/extraction/wasm',{recursive:true});fs.readdirSync('src/extraction/wasm').filter(f=>f.endsWith('.wasm')).forEach(f=>fs.copyFileSync('src/extraction/wasm/'+f,'dist/extraction/wasm/'+f));const tmplSrc='assets/claude-template';const tmplDest='dist/.claude-template';if(fs.existsSync(tmplSrc)){fs.rmSync(tmplDest,{recursive:true,force:true});fs.mkdirSync(tmplDest,{recursive:true});(function walk(from,to){for(const e of fs.readdirSync(from,{withFileTypes:true})){if(e.name==='node_modules'||e.name==='.DS_Store'||e.name.startsWith('.'))continue;const fp=path.join(from,e.name);const tp=path.join(to,e.name);if(e.isDirectory()){fs.mkdirSync(tp,{recursive:true});walk(fp,tp)}else if(e.isFile()){fs.copyFileSync(fp,tp)}}})(tmplSrc,tmplDest)}\"",
+    "dev": "tsc --watch",
+    "cli": "npm run build && node dist/bin/codegraph.js",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:eval": "vitest run __tests__/evaluation/",
+    "eval": "npm run build && npx tsx __tests__/evaluation/runner.ts",
+    "clean": "node -e \"const fs=require('fs');fs.rmSync('dist',{recursive:true,force:true})\"",
+    "prepublishOnly": "npm run build"
+  },
+  "keywords": [
+    "code-intelligence",
+    "knowledge-graph",
+    "static-analysis"
+  ],
+  "author": "",
+  "license": "MIT",
+  "dependencies": {
+    "@clack/prompts": "^1.3.0",
+    "commander": "^14.0.2",
+    "fast-string-width": "^3.0.2",
+    "fast-wrap-ansi": "^0.2.0",
+    "ignore": "^7.0.5",
+    "jsonc-parser": "^3.3.1",
+    "mysql2": "^3.11.0",
+    "pg": "^8.12.0",
+    "picomatch": "^4.0.3",
+    "sisteransi": "^1.0.5",
+    "tree-sitter-wasms": "^0.1.11",
+    "web-tree-sitter": "^0.25.3"
+  },
+  "devDependencies": {
+    "@types/better-sqlite3": "^7.6.0",
+    "@types/node": "^20.19.30",
+    "@types/pg": "^8.20.0",
+    "@types/picomatch": "^4.0.2",
+    "typescript": "^5.0.0",
+    "vitest": "^2.1.9"
+  },
+  "engines": {
+    "node": ">=20.0.0 <25.0.0"
+  }
+}