feat: add npx CLI with monorepo, CI/CD, and ephemeral worker architecture (#256)

* feat: integrate npx CLI, CI/CD, and ephemeral worker architecture

Bring in changes from shannon-npx: npx-distributable CLI package (cli/),
semantic-release CI/CD workflows, ephemeral per-scan worker containers,
TOML config support, setup wizard, and workspace management.

Preserves all shannon-only changes: security hardening (localhost-bound
ports, MCP env allowlist, path traversal guard), updated benchmarks
(XBEN 19/31/35/44), README assets, and prompt injection disclaimer.

Applies security hardening to cli/infra/compose.yml as well.

* refactor: migrate to Turborepo + pnpm + Biome monorepo

Restructure into apps/worker, apps/cli, packages/mcp-server with
Turborepo task orchestration, pnpm workspaces, Biome linting/formatting,
and tsdown CLI bundling.

Key changes:
- src/ -> apps/worker/src/, cli/ -> apps/cli/, mcp-server/ -> packages/mcp-server/
- prompts/ and configs/ moved into apps/worker/
- npm replaced with pnpm, package-lock.json replaced with pnpm-lock.yaml
- Dockerfile updated for pnpm-based builds
- CLI logs command rewritten with chokidar for cross-platform reliability
- Router health checking added for auto-detected router mode
- Centralized path resolution via apps/worker/src/paths.ts

* fix: resolve all biome warnings and formatting issues

- Remove unnecessary non-null assertions where values are guaranteed
- Replace array index access with .at() for safer element retrieval
- Use local variables to avoid repeated process.env lookups
- Replace any types with unknown in functional utilities
- Use nullish coalescing for TOTP hash byte access
- Auto-format security patches to match biome config

* fix: pin pnpm to 10.12.1 in Dockerfile for catalog support

* fix: handle Esc cancellation in Bedrock setup flow

Replace p.group() with individual prompts and per-field cancel checks,
matching the pattern used by all other provider setup flows.

* feat: add optional model customization to Anthropic setup

* fix: resolve Docker bind mount permission errors on Linux

Use entrypoint-based UID remapping instead of --user flag so the
container's pentest user matches the host UID/GID, keeping bind-mounted
volumes writable. Git config moved to --system level to survive remapping.

* fix: show resumed workflow ID in splash screen URL

When resuming a workflow, the Temporal Web UI link pointed to the old
(terminated) workflow ID. Now extracts "New Workflow ID" from the resume
header in workflow.log, falling back to the original ID for fresh scans.

* style: fix biome formatting in docker.ts

* fix: align TypeScript config types with JSON Schema

- SuccessCondition.type: use schema values (url_contains,
  element_present, url_equals_exactly, text_contains) instead of
  stale values (url, cookie, element, redirect)
- Authentication.login_flow: mark optional to match schema which
  does not require it

* feat: mark GitHub release as latest during rollback

* fix: use native ARM64 runners for Docker multi-platform builds

Replace QEMU emulation with parallel native builds using a matrix
strategy (ubuntu-latest for amd64, ubuntu-24.04-arm for arm64).
Each platform pushes by digest, then a merge job creates the
multi-arch manifest list before signing with cosign.

* fix: resolve SessionMutex race condition with 3+ concurrent waiters

* fix: skip POSIX permission check on Windows

writeFileSync mode option is ignored on Windows, so config.toml
gets 0o666 and the guard rejects it.

* fix: resolve unsubstituted placeholders in report prompt

Remove unused {{GITHUB_URL}} placeholder and wire up {{AUTH_CONTEXT}}
with structured auth context (login type, username, URL, MFA status).

* fix: remove duplicate environment gate from merge-docker job

Move DOCKERHUB_USERNAME from vars to secrets so merge-docker can access
credentials without its own environment scope. This eliminates the
redundant double approval since build-docker already gates on
release-publish.

* fix: replace POSIX sleep binary with cross-platform async sleep

execFileSync('sleep') is unavailable on Windows. Use node:timers/promises
setTimeout instead, making ensureInfra async.

* fix: use session.json for workflow ID on resume instead of parsing workflow.log

On resume, workflow.log already exists with stale headers from the
previous run. The CLI poll found '====' immediately and extracted the
old workflow ID, producing a wrong Temporal Web UI URL.

Read the workflow ID from session.json instead — the worker writes
resume attempts there atomically. For fresh runs, poll until
originalWorkflowId appears. For resumes, poll until a new
resumeAttempts entry is appended.

* feat: add custom base URL support for Anthropic-compatible proxies

Support ANTHROPIC_BASE_URL + ANTHROPIC_AUTH_TOKEN to route SDK requests
through LiteLLM or any Anthropic-compatible proxy. Adds TUI wizard
option, TOML config mapping, credential validation, and preflight
endpoint reachability check via SDK query.

* fix: remove environment gates and add NPM_TOKEN to publish step

* feat: add beta release and rollback workflows with cosign signing

* fix: remove redundant checkout and pnpm steps from beta release workflow

* docs: normalize README commands to mode-neutral shorthand

Add a substitution note after Quick Start sections so all subsequent
examples use bare `shannon` instead of mixing `./shannon` and
`npx @keygraph/shannon`. Mode-specific commands (build, update,
uninstall) get inline annotations. Also fixes a broken command in the
Custom Base URL section.

* fix: remove redundant `update` command

Image is already auto-pulled by `ensureImage()` during `start` when the
pinned version tag is missing locally. Manual `update` was unnecessary.

* docs: add CLI package README stub

* docs: update README setup instructions for dual CLI modes

* docs: update announcement banner to npx availability

* feat: migrate from MCP tools to CLI based tools (#252)

* feat: migrate from MCP tools to CLI tools

* fix: restore browser action emoji formatters for CLI output

Adapt formatBrowserAction for playwright-cli commands, replacing the old
mcp__playwright__browser_* tool name matching removed during migration.

* fix: mount credential file to fixed container path for Vertex AI

GOOGLE_APPLICATION_CREDENTIALS was forwarded as-is to the container,
causing the relative host path to resolve against the repo mount
instead of the credentials mount. Now both local and npx modes mount
the resolved file to /app/credentials/google-sa-key.json and rewrite
the env var to match.

* feat: add git awareness and optional description field to config

* fix: drop redundant --ipc host flag from worker container

* fix: align announcement banner URL with main branch

* feat: add target URL reachability preflight check (#254)

* Moving asset benchmark graph image to this folder

* Move benchmark results to benchmark repo

Windows Defender flags exploit code in the pentest reports as false positives, forcing every Windows user to add a Defender exclusion just to clone Shannon.

* Updated README

* fix: case-insensitive grep for semantic-release version probe

* fix: harden supply chain security (#255)

* fix: patch smol-toml and tsdown vulnerabilities

Update smol-toml 1.6.0→1.6.1 (DoS via recursive comment parsing) and
tsdown 0.21.2→0.21.5 (picomatch ReDoS + method injection).

* fix: pin all unpinned dependency versions in Dockerfile

Pins subfinder v2.13.0, WhatWeb v0.6.3 (switched from git clone to
release tarball), schemathesis 4.13.0, addressable 2.8.9,
claude-code 2.1.84, and playwright-cli 0.1.1 for reproducible builds.

* fix: pin GitHub Actions to commit SHAs for supply chain security

* fix: pin GitHub Actions to commit SHAs in beta and rollback workflows

apps/worker/src/utils/billing-detection.ts

@@ -0,0 +1,91 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * Consolidated billing/spending cap detection utilities.
+ *
+ * Anthropic's spending cap behavior is inconsistent:
+ * - Sometimes a proper SDK error (billing_error)
+ * - Sometimes Claude responds with text about the cap
+ * - Sometimes partial billing before cutoff
+ *
+ * This module provides defense-in-depth detection with shared pattern lists
+ * to prevent drift between detection points.
+ */
+
+/**
+ * Text patterns for SDK output sniffing (what Claude says).
+ * Used by message-handlers.ts and the behavioral heuristic.
+ */
+export const BILLING_TEXT_PATTERNS = [
+  'spending cap',
+  'spending limit',
+  'cap reached',
+  'budget exceeded',
+  'usage limit',
+  'resets',
+] as const;
+
+/**
+ * API patterns for error message classification (what the API returns).
+ * Used by classifyErrorForTemporal in error-handling.ts.
+ */
+export const BILLING_API_PATTERNS = [
+  'billing_error',
+  'credit balance is too low',
+  'insufficient credits',
+  'usage is blocked due to insufficient credits',
+  'please visit plans & billing',
+  'please visit plans and billing',
+  'usage limit reached',
+  'quota exceeded',
+  'daily rate limit',
+  'limit will reset',
+  'billing limit reached',
+] as const;
+
+/**
+ * Checks if text matches any billing text pattern.
+ * Used for sniffing SDK output content for spending cap messages.
+ */
+export function matchesBillingTextPattern(text: string): boolean {
+  const lowerText = text.toLowerCase();
+  return BILLING_TEXT_PATTERNS.some((pattern) => lowerText.includes(pattern));
+}
+
+/**
+ * Checks if an error message matches any billing API pattern.
+ * Used for classifying API error messages.
+ */
+export function matchesBillingApiPattern(message: string): boolean {
+  const lowerMessage = message.toLowerCase();
+  return BILLING_API_PATTERNS.some((pattern) => lowerMessage.includes(pattern));
+}
+
+/**
+ * Behavioral heuristic for detecting spending cap.
+ *
+ * When Claude hits a spending cap, it often returns a short message
+ * with $0 cost. Legitimate agent work NEVER costs $0 with only 1-2 turns.
+ *
+ * This combines three signals:
+ * 1. Very low turn count (<=2)
+ * 2. Zero cost ($0)
+ * 3. Text matches billing patterns
+ *
+ * @param turns - Number of turns the agent took
+ * @param cost - Total cost in USD
+ * @param resultText - The result text from the agent
+ * @returns true if this looks like a spending cap hit
+ */
+export function isSpendingCapBehavior(turns: number, cost: number, resultText: string): boolean {
+  // Only check if turns <= 2 AND cost is exactly 0
+  if (turns > 2 || cost !== 0) {
+    return false;
+  }
+
+  return matchesBillingTextPattern(resultText);
+}

apps/worker/src/utils/concurrency.ts

@@ -0,0 +1,60 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * Concurrency Control Utilities
+ *
+ * Provides mutex implementation for preventing race conditions during
+ * concurrent session operations.
+ */
+
+type UnlockFunction = () => void;
+
+/**
+ * SessionMutex - Promise-based mutex for session file operations
+ *
+ * Prevents race conditions when multiple agents or operations attempt to
+ * modify the same session data simultaneously. This is particularly important
+ * during parallel execution of vulnerability analysis and exploitation phases.
+ *
+ * Usage:
+ * ```ts
+ * const mutex = new SessionMutex();
+ * const unlock = await mutex.lock(sessionId);
+ * try {
+ *   // Critical section - modify session data
+ * } finally {
+ *   unlock(); // Always release the lock
+ * }
+ * ```
+ */
+// Promise-based mutex with chained queue semantics - safe for parallel agents on same session
+export class SessionMutex {
+  // Map of sessionId -> Promise (tail of the FIFO queue)
+  private locks: Map<string, Promise<void>> = new Map();
+
+  // Chain onto the queue tail, then wait for predecessor to release. Guarantees FIFO ordering.
+  async lock(sessionId: string): Promise<UnlockFunction> {
+    // 1. Capture the current tail of the queue
+    const prev = this.locks.get(sessionId) ?? Promise.resolve();
+
+    // 2. Create our lock and immediately become the new tail
+    let resolve: () => void;
+    const promise = new Promise<void>((r) => (resolve = r));
+    this.locks.set(sessionId, promise);
+
+    // 3. Wait for predecessor to release
+    await prev;
+
+    // 4. Return unlock that releases the next waiter in the chain
+    return () => {
+      if (this.locks.get(sessionId) === promise) {
+        this.locks.delete(sessionId);
+      }
+      resolve();
+    };
+  }
+}

apps/worker/src/utils/file-io.ts

@@ -0,0 +1,73 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * File I/O Utilities
+ *
+ * Core utility functions for file operations including atomic writes,
+ * directory creation, and JSON file handling.
+ */
+
+import fs from 'node:fs/promises';
+
+/**
+ * Ensure directory exists (idempotent, race-safe)
+ */
+export async function ensureDirectory(dirPath: string): Promise<void> {
+  try {
+    await fs.mkdir(dirPath, { recursive: true });
+  } catch (error) {
+    // Ignore EEXIST errors (race condition safe)
+    if ((error as NodeJS.ErrnoException).code !== 'EEXIST') {
+      throw error;
+    }
+  }
+}
+
+/**
+ * Atomic write using temp file + rename pattern
+ * Guarantees no partial writes or corruption on crash
+ */
+export async function atomicWrite(filePath: string, data: object | string): Promise<void> {
+  const tempPath = `${filePath}.tmp`;
+  const content = typeof data === 'string' ? data : JSON.stringify(data, null, 2);
+
+  try {
+    // Write to temp file
+    await fs.writeFile(tempPath, content, 'utf8');
+
+    // Atomic rename (POSIX guarantee: atomic on same filesystem)
+    await fs.rename(tempPath, filePath);
+  } catch (error) {
+    // Clean up temp file on failure
+    try {
+      await fs.unlink(tempPath);
+    } catch {
+      // Ignore cleanup errors
+    }
+    throw error;
+  }
+}
+
+/**
+ * Read and parse JSON file
+ */
+export async function readJson<T = unknown>(filePath: string): Promise<T> {
+  const content = await fs.readFile(filePath, 'utf8');
+  return JSON.parse(content) as T;
+}
+
+/**
+ * Check if file exists
+ */
+export async function fileExists(filePath: string): Promise<boolean> {
+  try {
+    await fs.access(filePath);
+    return true;
+  } catch {
+    return false;
+  }
+}

apps/worker/src/utils/formatting.ts

@@ -0,0 +1,60 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * Formatting Utilities
+ *
+ * Generic formatting functions for durations, timestamps, and percentages.
+ */
+
+/**
+ * Format duration in milliseconds to human-readable string
+ */
+export function formatDuration(ms: number): string {
+  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 = Math.floor(seconds % 60);
+  return `${minutes}m ${remainingSeconds}s`;
+}
+
+/**
+ * Format timestamp to ISO 8601 string
+ */
+export function formatTimestamp(timestamp: number = Date.now()): string {
+  return new Date(timestamp).toISOString();
+}
+
+/**
+ * Calculate percentage
+ */
+export function calculatePercentage(part: number, total: number): number {
+  if (total === 0) return 0;
+  return (part / total) * 100;
+}
+
+/**
+ * Extract agent type from description string for display purposes
+ */
+export function extractAgentType(description: string): string {
+  if (description.includes('Pre-recon')) {
+    return 'pre-reconnaissance';
+  }
+  if (description.includes('Recon')) {
+    return 'reconnaissance';
+  }
+  if (description.includes('Report')) {
+    return 'report generation';
+  }
+  return 'analysis';
+}

apps/worker/src/utils/functional.ts

@@ -0,0 +1,26 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * Functional Programming Utilities
+ *
+ * Generic functional composition patterns for async operations.
+ */
+
+// biome-ignore lint/suspicious/noExplicitAny: pipeline functions need flexible typing for composition
+type PipelineFunction = (x: any) => any | Promise<any>;
+
+/**
+ * Async pipeline that passes result through a series of functions.
+ * Clearer than reduce-based pipe and easier to debug.
+ */
+export async function asyncPipe<TResult>(initial: unknown, ...fns: PipelineFunction[]): Promise<TResult> {
+  let result = initial;
+  for (const fn of fns) {
+    result = await fn(result);
+  }
+  return result as TResult;
+}

apps/worker/src/utils/metrics.ts

@@ -0,0 +1,26 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+export class Timer {
+  name: string;
+  startTime: number;
+  endTime: number | null = null;
+
+  constructor(name: string) {
+    this.name = name;
+    this.startTime = Date.now();
+  }
+
+  stop(): number {
+    this.endTime = Date.now();
+    return this.duration();
+  }
+
+  duration(): number {
+    const end = this.endTime || Date.now();
+    return end - this.startTime;
+  }
+}