gitnexus 1.6.6-rc.2 → 1.6.6-rc.4

package/dist/cli/analyze.js

@@ -12,6 +12,7 @@ import { execFileSync } from 'child_process';
 import v8 from 'v8';
 import cliProgress from 'cli-progress';
 import { closeLbug } from '../core/lbug/lbug-adapter.js';
+import { isWalCorruptionError, WAL_RECOVERY_SUGGESTION } from '../core/lbug/lbug-config.js';
 import { getStoragePaths, getGlobalRegistryPath, RegistryNameCollisionError, AnalysisNotFinalizedError, assertAnalysisFinalized, } from '../storage/repo-manager.js';
 import { getGitRoot, hasGitDir } from '../storage/git.js';
 import { runFullAnalysis } from '../core/run-analyze.js';
@@ -468,6 +469,16 @@ export const analyzeCommand = async (inputPath, options) => {
             process.exitCode = 1;
             return;
         }
+        // WAL corruption — the index file is unreadable. Give a clear recovery
+        // path without a confusing stack trace (the native error message alone
+        // is enough signal).
+        if (isWalCorruptionError(err) || msg.includes('LadybugDB WAL corruption')) {
+            cliError(`  The GitNexus index has a corrupted WAL file.\n` +
+                `  This usually happens when a previous analysis was interrupted mid-write.\n` +
+                `  ${WAL_RECOVERY_SUGGESTION}\n`, { recoveryHint: 'wal-corruption' });
+            process.exitCode = 1;
+            return;
+        }
         // HF download failure — show clean guidance without the raw stack trace.
         // Checked before writeFatalToStderr so the user sees one focused message
         // rather than a stack-trace dump followed by a second remediation block.

package/dist/cli/index.js

@@ -103,7 +103,7 @@ program
     .option('--reasoning-model', 'Mark deployment as reasoning model (o1/o3/o4-mini) — strips temperature, uses max_completion_tokens')
     .option('--no-reasoning-model', 'Disable reasoning model mode (overrides saved config)')
     .option('--concurrency <n>', 'Parallel LLM calls (default: 3)', '3')
-    .option('--timeout <seconds>', 'Per-attempt LLM request timeout in seconds (default: 60)')
+    .option('--timeout <seconds>', 'LLM request timeout in seconds (default: disabled)')
     .option('--retries <n>', 'Max LLM retry attempts per request (default: 3)')
     .option('--gist', 'Publish wiki as a public GitHub Gist after generation')
     .option('-v, --verbose', 'Enable verbose output (show LLM commands and responses)')

package/dist/cli/serve.js

@@ -1,6 +1,7 @@
 import { createServer } from '../server/api.js';
 import { logger, flushLoggerSync } from '../core/logger.js';
 import { cliError } from './cli-message.js';
+import { isWalCorruptionError, WAL_RECOVERY_SUGGESTION } from '../core/lbug/lbug-config.js';
 // Catch anything that would cause a silent exit. Pino v10's default
 // destination is `sync: false` (SonicBoom buffered) — call
 // `flushLoggerSync()` between the log and `process.exit(1)` so the crash
@@ -32,7 +33,11 @@ export const serveCommand = async (options) => {
         await createServer(port, host);
     }
     catch (err) {
-        if (err.code === 'EADDRINUSE') {
+        if (isWalCorruptionError(err)) {
+            cliError(`\nGitNexus server could not start: the index has a corrupted WAL file.\n` +
+                `  ${WAL_RECOVERY_SUGGESTION}\n`, { recoveryHint: 'wal-corruption' });
+        }
+        else if (err.code === 'EADDRINUSE') {
             cliError(`\nFailed to start GitNexus server:\n` +
                 `  ${err.message || err}\n\n` +
                 `  Port ${port} is already in use. Either:\n` +

package/dist/cli/wiki.js

@@ -14,6 +14,19 @@ import { WikiGenerator } from '../core/wiki/generator.js';
 import { resolveLLMConfig } from '../core/wiki/llm-client.js';
 import { detectCursorCLI } from '../core/wiki/cursor-client.js';
 import { logger } from '../core/logger.js';
+function parsePositiveIntegerOption(value, flag, multiplier = 1) {
+    if (value === undefined)
+        return undefined;
+    const trimmed = value.trim();
+    if (!/^[1-9]\d*$/.test(trimmed)) {
+        throw new Error(`${flag} must be a positive integer`);
+    }
+    const parsed = parseInt(trimmed, 10);
+    if (parsed > Math.floor(Number.MAX_SAFE_INTEGER / multiplier)) {
+        throw new Error(`${flag} is too large`);
+    }
+    return parsed;
+}
 /**
  * Prompt the user for input via stdin.
  */
@@ -100,6 +113,17 @@ export const wikiCommand = async (inputPath, options) => {
         process.exitCode = 1;
         return;
     }
+    let timeoutSeconds;
+    let retries;
+    try {
+        timeoutSeconds = parsePositiveIntegerOption(options?.timeout, '--timeout', 1000);
+        retries = parsePositiveIntegerOption(options?.retries, '--retries');
+    }
+    catch (error) {
+        console.log(`  Error: ${error.message}\n`);
+        process.exitCode = 1;
+        return;
+    }
     // ── Resolve LLM config (with interactive fallback) ─────────────────
     // Save any CLI overrides immediately
     if (options?.apiKey ||
@@ -305,15 +329,11 @@ export const wikiCommand = async (inputPath, options) => {
         }
     }
     // ── Apply per-run overrides not saved to config ────────────────────
-    if (options?.timeout) {
-        const secs = parseInt(options.timeout, 10);
-        if (!isNaN(secs) && secs > 0)
-            llmConfig.requestTimeoutMs = secs * 1000;
+    if (timeoutSeconds !== undefined) {
+        llmConfig.requestTimeoutMs = timeoutSeconds * 1000;
     }
-    if (options?.retries) {
-        const n = parseInt(options.retries, 10);
-        if (!isNaN(n) && n > 0)
-            llmConfig.maxAttempts = n;
+    if (retries !== undefined) {
+        llmConfig.maxAttempts = retries;
     }
     // ── Setup progress bar with elapsed timer ──────────────────────────
     const bar = new cliProgress.SingleBar({
@@ -473,6 +493,9 @@ export const wikiCommand = async (inputPath, options) => {
         if (err.message?.includes('No source files')) {
             console.log(`\n  ${err.message}\n`);
         }
+        else if (err.message?.includes('LLM request timed out after')) {
+            console.log(`\n  Timeout: ${err.message}\n`);
+        }
         else if (err.message?.includes('content filter')) {
             // Content filter block — actionable message
             console.log(`\n  Content Filter: ${err.message}\n`);

package/dist/core/lbug/lbug-adapter.js

@@ -8,7 +8,7 @@ import lbug from '@ladybugdb/core';
 import { NODE_TABLES, REL_TABLE_NAME, SCHEMA_QUERIES, EMBEDDING_TABLE_NAME, STALE_HASH_SENTINEL, } from './schema.js';
 import { streamAllCSVsToDisk } from './csv-generator.js';
 import { extensionManager } from './extension-loader.js';
-import { closeLbugConnection, isDbBusyError, isOpenRetryExhausted, openLbugConnection, waitForWindowsHandleRelease, } from './lbug-config.js';
+import { closeLbugConnection, isDbBusyError, isOpenRetryExhausted, isWalCorruptionError, openLbugConnection, WAL_RECOVERY_SUGGESTION, waitForWindowsHandleRelease, } from './lbug-config.js';
 import { isVectorExtensionSupportedByPlatform } from '../platform/capabilities.js';
 import { logger } from '../logger.js';
 /**
@@ -508,6 +508,22 @@ const doInitLbug = async (dbPath) => {
             //     anyway and any genuine cross-process lock contention surfaces
             //     on the next operation via withLbugDb's retry. Logging it here
             //     would just be noise in CI.
+            //
+            // WAL corruption: the first DDL write after DB open triggers WAL
+            // replay — if the WAL file was left in a corrupt state by an
+            // interrupted previous run, the native engine throws here. Rather
+            // than logging a WARN and continuing in a broken state, close the
+            // DB cleanly and surface an actionable error so the caller (serve,
+            // MCP, analyze) can exit with a clear recovery message.
+            if (isWalCorruptionError(err)) {
+                await safeClose();
+                currentDbPath = null;
+                ftsLoaded = false;
+                vectorExtensionLoaded = false;
+                ensuredFTSIndexes.clear();
+                throw new Error(`LadybugDB WAL corruption detected at ${dbPath}. ${WAL_RECOVERY_SUGGESTION}\n` +
+                    `  Original error: ${msg.slice(0, 200)}`);
+            }
             if (!msg.includes('already exists') && !isDbBusyError(err)) {
                 logger.warn(`⚠️ Schema creation warning: ${msg.slice(0, 120)}`);
             }

package/dist/core/lbug/lbug-config.d.ts

@@ -32,7 +32,7 @@ import type lbug from '@ladybugdb/core';
  * integer; anything invalid falls back to the default.
  */
 export declare const LBUG_MAX_DB_SIZE: number;
-export declare const WAL_RECOVERY_SUGGESTION = "WAL corruption detected. Run `gitnexus analyze` to rebuild the index.";
+export declare const WAL_RECOVERY_SUGGESTION = "WAL corruption detected. Run `gitnexus analyze --force` to rebuild the index.";
 export declare function isWalCorruptionError(err: unknown): boolean;
 type LbugModule = typeof lbug;
 export interface LbugDatabaseOptions {

package/dist/core/lbug/lbug-config.js

@@ -44,7 +44,7 @@ export const LBUG_MAX_DB_SIZE = (() => {
 })();
 /** Matches WAL corruption errors from the LadybugDB engine. */
 const WAL_CORRUPTION_RE = /corrupt(ed)?\s+wal|invalid\s+wal\s+record|wal.*corrupt|checksum.*wal/i;
-export const WAL_RECOVERY_SUGGESTION = 'WAL corruption detected. Run `gitnexus analyze` to rebuild the index.';
+export const WAL_RECOVERY_SUGGESTION = 'WAL corruption detected. Run `gitnexus analyze --force` to rebuild the index.';
 export function isWalCorruptionError(err) {
     if (!err)
         return false;

package/dist/core/lbug/pool-adapter.js

@@ -17,7 +17,7 @@
 import fs from 'fs/promises';
 import lbug from '@ladybugdb/core';
 import { loadFTSExtension } from './lbug-adapter.js';
-import { createLbugDatabase, isWalCorruptionError } from './lbug-config.js';
+import { createLbugDatabase, isWalCorruptionError, WAL_RECOVERY_SUGGESTION, } from './lbug-config.js';
 const pool = new Map();
 const poolCloseListeners = new Set();
 /**
@@ -310,8 +310,7 @@ async function doInitLbug(repoId, dbPath) {
                         break;
                     }
                     catch (retryErr) {
-                        throw new Error(`LadybugDB WAL corruption detected for ${repoId}. ` +
-                            `Run \`gitnexus analyze\` to rebuild the index. ` +
+                        throw new Error(`LadybugDB WAL corruption detected for ${repoId}. ${WAL_RECOVERY_SUGGESTION} ` +
                             `(${retryErr instanceof Error ? retryErr.message : String(retryErr)})`);
                     }
                 }

package/dist/core/wiki/llm-client.d.ts

@@ -19,7 +19,7 @@ export interface LLMConfig {
     apiVersion?: string;
     /** When true, strips sampling params and uses max_completion_tokens instead of max_tokens */
     isReasoningModel?: boolean;
-    /** Per-attempt fetch timeout in ms (default: 60_000). */
+    /** Per-attempt fetch timeout in ms. Omit to disable request timeouts. */
     requestTimeoutMs?: number;
     /** Max fetch attempts before giving up (default: 3). */
     maxAttempts?: number;

package/dist/core/wiki/llm-client.js

@@ -38,6 +38,19 @@ export async function resolveLLMConfig(overrides) {
 export function estimateTokens(text) {
     return Math.ceil(text.length / 4);
 }
+function formatTimeoutDuration(timeoutMs) {
+    if (timeoutMs >= 1000 && timeoutMs % 1000 === 0) {
+        return `${timeoutMs / 1000}s`;
+    }
+    return `${timeoutMs}ms`;
+}
+function isTimeoutLikeError(err) {
+    if (!(err instanceof Error))
+        return false;
+    if (err.name === 'TimeoutError' || err.name === 'AbortError')
+        return true;
+    return /time(d)?\s*out|timeout/i.test(err.message);
+}
 /**
  * Validate that a base URL supplied for LLM API calls is a safe HTTP/HTTPS
  * endpoint (CWE-918 / CodeQL js/http-to-file-access).
@@ -166,12 +179,12 @@ export async function callLLM(prompt, config, systemPrompt, options) {
                 ...authHeaders,
             },
             body: JSON.stringify(body),
-            // Per-attempt timeout. Without this each retry can hang
-            // indefinitely on a frozen TCP connection — the per-call
-            // signal is the only timeout `resilientFetch` honors;
-            // `capDelayMs` only bounds the *backoff* between attempts.
-            // Default 60s; raise via --timeout for slow models or large pages.
-            signal: AbortSignal.timeout(config.requestTimeoutMs ?? 60_000),
+            // Request timeout is opt-in for wiki generation. Large local
+            // model runs can legitimately take well over a minute, so the
+            // default runtime path must not impose a hidden 60s ceiling.
+            signal: config.requestTimeoutMs !== undefined
+                ? AbortSignal.timeout(config.requestTimeoutMs)
+                : undefined,
         }, {
             breakerKey: `wiki-llm-${new URL(url).host}`,
             retry: { maxAttempts: config.maxAttempts ?? 3, baseDelayMs: 2_000, capDelayMs: 30_000 },
@@ -185,6 +198,10 @@ export async function callLLM(prompt, config, systemPrompt, options) {
             const errorText = await err.response.text().catch(() => 'unknown error');
             throw new Error(`LLM API error (${err.response.status} after retries): ${errorText.slice(0, 500)}`);
         }
+        if (config.requestTimeoutMs !== undefined && isTimeoutLikeError(err)) {
+            throw new Error(`LLM request timed out after ${formatTimeoutDuration(config.requestTimeoutMs)}. ` +
+                'Increase --timeout or omit it to disable the request timeout.');
+        }
         throw err;
     }
     if (!response.ok) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.6-rc.2",
+  "version": "1.6.6-rc.4",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",