shannon/CLAUDE.md

CLAUDE.md

AI-powered penetration testing agent for defensive security analysis. Automates vulnerability assessment by combining reconnaissance tools with AI-powered code analysis.

Commands

Prerequisites: Docker, AI provider credentials (.env for local, npx @keygraph/shannon setup or env vars for npx)

Dual CLI

Shannon supports two CLI modes, auto-detected based on the current working directory:

	npx (npx @keygraph/shannon)	Local (./shannon)
Install	Zero-install via npm	Clone the repo
Image	Pulled from Docker Hub (keygraph/shannon:latest)	Built locally (shannon-worker)
State	~/.shannon/	Project directory
Credentials	~/.shannon/config.toml (via npx @keygraph/shannon setup) or env vars	./.env
Config	~/.shannon/config.toml (via npx @keygraph/shannon setup)	N/A
Prompts	Bundled in Docker image	Mounted from ./apps/worker/prompts/ (live-editable)

Mode auto-detection: local mode activates when env var SHANNON_LOCAL=1 is set by the ./shannon entry point (apps/cli/src/mode.ts). Otherwise npx mode.

npx Quick Start

# Configure credentials (interactive wizard)
npx @keygraph/shannon setup

# Or export env vars directly (non-interactive / CI)
export ANTHROPIC_API_KEY=your-key

# Run
npx @keygraph/shannon start -u <url> -r /path/to/repo

Local (Development) Quick Start

# Setup
echo "ANTHROPIC_API_KEY=your-key" > .env

# Build (auto-runs if image missing)
./shannon build

# Run
./shannon start -u <url> -r my-repo
./shannon start -u <url> -r my-repo -c ./apps/worker/configs/my-config.yaml
./shannon start -u <url> -r /any/path/to/repo

Common Commands

# Setup (npx mode only — one-time credential configuration)
npx @keygraph/shannon setup

# Workspaces & Resume
./shannon start -u <url> -r my-repo -w my-audit    # New named workspace
./shannon start -u <url> -r my-repo -w my-audit    # Resume (same command)
./shannon workspaces                                 # List all workspaces

# Monitor
./shannon logs <workspace>            # Show a scan's live log
./shannon status                      # Show running scans
# Dashboard: http://localhost:8233

# Stop
./shannon stop                        # Preserves scan data
./shannon stop --clean                # Full cleanup including volumes (confirms first; --yes/-y to skip)

# Version
./shannon version                     # npx: package version; local: git SHA

# Image management
./shannon build [--no-cache]          # Local mode: build worker image
npx @keygraph/shannon uninstall             # npx mode: remove ~/.shannon/ (confirms first; --yes/-y to skip)

# Build TypeScript (development)
pnpm run build                       # Build all packages via Turborepo
pnpm run check                       # Type-check all packages
pnpm biome                           # Biome lint + format + import sorting check
pnpm biome:fix                       # Auto-fix lint, format, and import sorting

Monorepo tooling: pnpm workspaces, Turborepo for task orchestration, Biome for linting/formatting. TypeScript compiler options shared via tsconfig.base.json at the root. All packages extend it, overriding only rootDir and outDir. Shared devDependencies (typescript, @types/node, turbo, @biomejs/biome) are hoisted to the root workspace.

Options: -c <file> (YAML config), -o <path> (output directory), -w <name> (named workspace; auto-resumes if exists), --pipeline-testing (minimal prompts, 10s retries), --debug (preserve worker container after exit for log inspection), --yes/-y (skip the confirmation prompt on stop --clean/uninstall; required for non-interactive use)

Architecture

Monorepo Layout

apps/cli/        — @keygraph/shannon (published to npm, bundled with tsdown)
apps/worker/     — @shannon/worker (private, Temporal worker + pipeline logic)

CLI Package (apps/cli/)

Published as @keygraph/shannon on npm. Contains only Docker orchestration logic — no Temporal SDK, business logic, or prompts. Bundled with tsdown for single-file ESM output.

• apps/cli/src/index.ts — CLI dispatcher (setup, start, stop, logs, workspaces, status, build, uninstall, version)
• apps/cli/src/mode.ts — Auto-detection: local mode if SHANNON_LOCAL=1 env var is set
• apps/cli/src/docker.ts — Compose lifecycle, image pull/build, ephemeral docker run worker spawning
• apps/cli/src/home.ts — State directory management (~/.shannon/ for npx, ./ for local)
• apps/cli/src/env.ts — .env loading, TOML fallback (npx only) via apps/cli/src/config/resolver.ts, credential validation, provider-scoped env flag building
• apps/cli/src/model-spec.ts — SHANNON_AI_MODEL (<provider>:<model-id>) parsing; mirrors apps/worker/src/ai/models.ts
• apps/cli/src/config/resolver.ts — Cascading config (npx only): env vars → ~/.shannon/config.toml (parsed with smol-toml)
• apps/cli/src/config/writer.ts — TOML serialization and secure file persistence (0o600)
• apps/cli/src/commands/setup.ts — Interactive TUI wizard (@clack/prompts) for provider credential setup (npx only)
• apps/cli/src/paths.ts — Repo/config path resolution (bare name → ./repos/<name>, or any absolute/relative path)
• apps/cli/src/version.ts — Version reporting (npx: package.json version; local: git-<sha>)
• apps/cli/src/tty.ts — Terminal capability detection: requireInteractive guard (fails fast off-TTY instead of hanging on a prompt), supportsColor color gating (NO_COLOR/FORCE_COLOR), and stdoutIsTerminal for spinner/cursor output
• apps/cli/src/commands/ — Command handlers
• apps/cli/infra/compose.yml — Bundled Temporal compose file for npx mode
• apps/cli/tsdown.config.ts — tsdown bundler config
• shannon — Node.js entry point (#!/usr/bin/env node) that delegates to apps/cli/dist/index.mjs

Docker Architecture

Infra (Temporal) runs via docker-compose.yml. Workers are ephemeral docker run --rm containers, one per scan, each with a unique task queue and isolated volume mounts.

• docker-compose.yml — Infra only: shannon-temporal (port 7233/8233). Network: shannon-net
• Dockerfile — 2-stage build (builder + Chainguard Wolfi runtime). Uses pnpm. Entrypoint: CMD ["node", "apps/worker/dist/temporal/worker.js"]
• No docker-compose.docker.yml — host gateway handled via --add-host flag in CLI
• /etc/hosts forwarding — at worker spawn, forwardEtcHostsFlags in apps/cli/src/docker.ts reads the host's /etc/hosts and emits one --add-host flag per valid user-added entry. Loopback IPs (127.x, ::1) are rewritten to host-gateway; IPv6 addresses are bracketed. Disable per-scan via SHANNON_FORWARD_HOSTS=false. No-op on Windows native (WSL2 reads its own /etc/hosts via the Linux path).

Worker Package (apps/worker/)

• apps/worker/src/paths.ts — Centralized path constants (PROMPTS_DIR, CONFIGS_DIR, WORKSPACES_DIR)
• apps/worker/src/session-manager.ts — Agent definitions (AGENTS record). Agent types in apps/worker/src/types/agents.ts
• apps/worker/src/config-parser.ts — YAML config parsing with JSON Schema validation
• apps/worker/src/ai/pi/pi-executor.ts — pi harness integration (agent-level retry disabled so Temporal owns restarts; provider-level retry on, see apps/worker/src/ai/pi/retry-settings.ts)
• apps/worker/src/services/ — Business logic layer (Temporal-agnostic). Activities delegate here. Key: agent-execution.ts, error-handling.ts, container.ts
• apps/worker/src/types/ — Consolidated types: Result<T,E>, ErrorCode, AgentName, ActivityLogger, etc.
• apps/worker/src/utils/ — Shared utilities (file I/O, formatting, concurrency)

Temporal Orchestration

Durable workflow orchestration with crash recovery, queryable progress, intelligent retry, and parallel execution (5 concurrent agents in vuln/exploit phases).

• apps/worker/src/temporal/workflows.ts — Main workflow (pentestPipelineWorkflow)
• apps/worker/src/temporal/activities.ts — Thin wrappers — heartbeat loop, error classification, container lifecycle. Business logic delegated to apps/worker/src/services/
• apps/worker/src/temporal/activity-logger.ts — TemporalActivityLogger implementation of ActivityLogger interface
• apps/worker/src/temporal/summary-mapper.ts — Maps PipelineSummary to WorkflowSummary
• apps/worker/src/temporal/worker.ts — Combined worker + client entry point (per-invocation task queue, submits workflow, waits for result)
• apps/worker/src/temporal/shared.ts — Types, interfaces, query definitions

Five-Phase Pipeline

1. Pre-Recon (pre-recon) — Source code analysis to build the architectural baseline
2. Recon (recon) — Attack surface mapping from initial findings
3. Vulnerability Analysis (5 parallel agents) — injection, xss, auth, authz, ssrf
4. Exploitation (5 parallel agents, conditional) — Exploits confirmed vulnerabilities
5. Reporting (report) — Executive-level security report

Supporting Systems

• Configuration — YAML configs in apps/worker/configs/ with JSON Schema validation (config-schema.json). Supports auth settings (MFA/TOTP), URL/code rule scoping (rules.avoid/rules.focus), run-scope steering (vuln_classes, exploit), free-form rules_of_engagement, and post-hoc report options (min_severity, min_confidence, guidance, and sarif to emit a SARIF 2.1.0 log via apps/worker/src/services/sarif-renderer.ts; exploit-only). code_path avoid rules are enforced via the @gotgenes/pi-permission-system extension: apps/worker/src/temporal/activities.ts:syncCodePathDenyRules writes a global path deny config once per workflow (apps/worker/src/ai/pi/permission-system.ts:syncPermissionSystemConfig), and the executor loads the extension when that config is present (apps/worker/src/ai/pi/pi-executor.ts), so denies fire across every tool and child task session. vuln_classes/exploit scope is locked into session.json on first run; resumes with a different scope fail fast (persistOrValidateRunScope). Credential resolution — local mode: env vars → ./.env; npx mode: env vars → ~/.shannon/config.toml (via npx @keygraph/shannon setup)
• Prompts — Per-phase templates in apps/worker/prompts/ with variable substitution ({{TARGET_URL}}, {{CONFIG_CONTEXT}}). Shared partials in apps/worker/prompts/shared/ via apps/worker/src/services/prompt-manager.ts, including _code-path-rules.txt (focus/avoid [FILE]/[GLOB] routing) and _rules-of-engagement.txt (free-text engagement rules). When exploit: false, apps/worker/src/services/findings-renderer.ts deterministically converts each *_exploitation_queue.json into a *_findings.md for report assembly — no LLM in the loop
• Agent Harness (pi) — Uses the pi harness (@earendil-works/pi-coding-agent, requires Node ≥ 22.19) via apps/worker/src/ai/pi/pi-executor.ts (runPiPrompt → createAgentSession). Retry is split in apps/worker/src/ai/pi/retry-settings.ts: pi's agent-level loop is off so Temporal owns agent restarts, while provider.maxRetries stays on — pi reads the provider block independently of the enabled flag — so transport faults are absorbed in-session rather than costing a full agent re-run. maxRetryDelayMs is left at pi's 60s default. One model runs every phase, named by SHANNON_AI_MODEL=<provider>:<model-id> (default anthropic:claude-sonnet-4-6). apps/worker/src/ai/models.ts parses the spec — splitting on the first colon only, so Bedrock IDs keep theirs — and resolves it through pi's ModelRuntime. pi ships the CredentialStore interface but no in-memory implementation (its own reads auth.json from disk), so RuntimeCredentialStore in that file supplies one: credentials arrive as env vars in an ephemeral container and must never touch disk. createModelRuntime(providerId, apiKey) builds the runtime; allowModelNetwork stays at its default false so a scan never blocks on a catalog refresh. resolveModelSelection() is async because ModelRuntime.create() is. Supported providers (all pi-ai provider ids): anthropic, openai, xai, amazon-bedrock. Each provider's API key env var is declared once in PROVIDER_API_KEY_ENV — Shannon uses each vendor's own variable name (OPENAI_API_KEY, XAI_API_KEY, …), never an invented one; Bedrock's entry is AWS_BEARER_TOKEN_BEDROCK, paired with AWS_REGION, which preflight requires separately as provider config rather than a credential. SHANNON_AI_BASE_URL overrides the endpoint for any provider (proxies/gateways); the credential is unchanged. pointAtGateway (apps/worker/src/ai/models.ts) applies the one dialect change: behind a base URL, openai follows SHANNON_AI_OPENAI_FORMAT (chat-completions default, or responses). On chat-completions it switches the API to openai-completions and drops the catalogue's Responses-shaped compat block so pi's detectCompat derives completions settings; on responses the descriptor is unchanged but for the endpoint. resolveGatewayFormat rejects the variable when the provider is not openai or no base URL is set, since it cannot take effect there. All other providers keep their API. The CLI mirrors the accepted values in apps/cli/src/model-spec.ts, forwards the variable in COMMON_FORWARD_VARS, and maps it to openai.format in config.toml. buildEnvFlags forwards only the selected provider's credential into the worker container. The CLI mirrors the parse rule and the provider/credential tables in apps/cli/src/model-spec.ts (it cannot import from the worker package); the two must stay in sync. pi ships no JSON-schema output or Task/TodoWrite built-ins, so structured queues are captured via a submit_exploitation_queue custom tool (apps/worker/src/ai/queue-schemas.ts), and task (child sessions scoped to read, grep, find, ls, write, and bash — no nested task or collector tools; CHILD_TOOLS in apps/worker/src/ai/pi/task-tool.ts) + todo_write (apps/worker/src/ai/pi/session-tools.ts) are provided as custom tools; the per-phase collectors are pi custom tools (TypeBox defineTool in apps/worker/src/collectors/). Shannon sets no thinking configuration at all — no thinkingLevel is passed to any createAgentSession call, so pi's own default applies. There is no adaptive-thinking support and no CLAUDE_ADAPTIVE_THINKING / core.adaptive_thinking setting. Browser automation via playwright-cli with session isolation (-s=<session>). TOTP generation via generate-totp CLI tool. Login flow template at apps/worker/prompts/shared/login-instructions.txt supports form, SSO, API, and basic auth. On authenticated whitebox scans, the validate-authentication preflight performs the single real login and saves the browser session to auth-state.json in the per-session audit directory (path from authStateFile() in apps/worker/src/audit/utils.ts, derived from generateAuditPath()). The validation activity (apps/worker/src/services/validate-authentication.ts) removes any stale file from a prior run before the agent runs and verifies the file parses and contains cookies or storage before the preflight is marked complete; logWorkflowComplete deletes it when the workflow ends so authenticated cookies don't sit on disk between scans. Agent prompts opt in to session reuse by @include(shared/_shared-session.txt) before their <login_instructions> block — the partial restores the session and falls through to the full login flow if verification fails. vuln-auth/exploit-auth omit the include and own their own login
• Audit System — Crash-safe append-only logging in workspaces/{hostname}_{sessionId}/. The run directory's top level holds only the human-facing report (Security-Assessment-Report.md, FINAL_REPORT_FILENAME in apps/worker/src/paths.ts); everything else — deliverables, per-agent logs, prompts, session.json, workflow.log, and browser artifacts — is nested under a hidden .shannon/ internals dir (INTERNAL_DIR) so a customer sees only the report. Audit path helpers route through generateInternalPath (apps/worker/src/audit/utils.ts); the CLI nests the overlay backing dirs under the same .shannon/ (apps/cli/src/docker.ts, start.ts). session.json/workflow.log reads use dual-read resolvers (resolveSessionJsonPath, resolveRunFile) that prefer .shannon/ and fall back to the legacy run-root layout, so pre-restructure workspaces stay listable (workspaces/logs) without migration. Resuming a pre-restructure workspace upgrades it in place first: migrateLegacyWorkspaceLayout (apps/cli/src/commands/start.ts) renames the flat deliverables/logs/session entries into .shannon/ (carrying the deliverables .git along) before the overlay dirs are mounted, so resume finds the old checkpoints instead of re-running every agent. The report is surfaced by copying the assembled comprehensive_security_assessment_report.md from the deliverables dir to the run root (copyReportToRunRoot in apps/worker/src/services/reporting.ts). WorkflowLogger (apps/worker/src/audit/workflow-logger.ts) provides unified human-readable per-workflow logs, backed by LogStream (apps/worker/src/audit/log-stream.ts) shared stream primitive
• Deliverables — Saved to .shannon/deliverables/ in the target repo via the save-deliverable CLI script (apps/worker/src/scripts/save-deliverable.ts)
• Workspaces & Resume — Named workspaces via -w <name> or auto-named from URL+timestamp. Resume detects completed agents via session.json. loadResumeState() in apps/worker/src/temporal/activities.ts validates deliverable existence, restores git checkpoints, and cleans up incomplete deliverables. Workspace listing via apps/worker/src/temporal/workspaces.ts

Development Notes

Adding a New Agent

1. Define agent in apps/worker/src/session-manager.ts (add to AGENTS record). ALL_AGENTS/AgentName types live in apps/worker/src/types/agents.ts
2. Create prompt template in apps/worker/prompts/ (e.g., vuln-newtype.txt)
3. Two-layer pattern: add a thin activity wrapper in apps/worker/src/temporal/activities.ts (heartbeat + error classification). AgentExecutionService in apps/worker/src/services/agent-execution.ts handles the agent lifecycle automatically via the AGENTS registry
4. Register activity in apps/worker/src/temporal/workflows.ts within the appropriate phase

Modifying Prompts

• Variable substitution: {{TARGET_URL}}, {{CONFIG_CONTEXT}}, {{LOGIN_INSTRUCTIONS}}
• Shared partials in apps/worker/prompts/shared/ included via apps/worker/src/services/prompt-manager.ts
• Test with --pipeline-testing for fast iteration

Key Design Patterns

• Configuration-Driven — YAML configs with JSON Schema validation
• Progressive Analysis — Each phase builds on previous results
• Harness-First — the pi harness (@earendil-works/pi-coding-agent) handles autonomous analysis
• Modular Error Handling — ErrorCode enum, Result<T,E> for explicit error propagation, automatic retry (3 attempts per agent)
• Services Boundary — Activities are thin Temporal wrappers; apps/worker/src/services/ owns business logic, accepts ActivityLogger, returns Result<T,E>. No Temporal imports in services
• DI Container — Per-workflow in apps/worker/src/services/container.ts. AuditSession excluded (parallel safety)
• Ephemeral Workers — Each scan runs in its own docker run --rm container with a per-invocation task queue. Temporal routes activities by queue name, so per-scan queues ensure activities never land on a worker with the wrong repo mounted

Security

Defensive security tool only. Use only on systems you own or have explicit permission to test.

Code Style Guidelines

Formatting

Biome handles formatting and linting. Run pnpm biome:fix to auto-fix. Config in biome.json: single quotes, semicolons, trailing commas, 2-space indent, 120 char line width.

Clarity Over Brevity

• Optimize for readability, not line count — three clear lines beat one dense expression
• Use descriptive names that convey intent
• Prefer explicit logic over clever one-liners

Structure

• Keep functions focused on a single responsibility
• Use early returns and guard clauses instead of deep nesting
• Never use nested ternary operators — use if/else or switch
• Extract complex conditions into well-named boolean variables

TypeScript Conventions

• Use function keyword for top-level functions (not arrow functions)
• Explicit return type annotations on exported/top-level functions
• Prefer readonly for data that shouldn't be mutated
• exactOptionalPropertyTypes is enabled — use spread for optional props, not direct undefined assignment

Avoid

• Combining multiple concerns into a single function to "save lines"
• Dense callback chains when sequential logic is clearer
• Sacrificing readability for DRY — some repetition is fine if clearer
• Abstractions for one-time operations
• Backwards-compatibility shims, deprecated wrappers, or re-exports for removed code — delete the old code, don't preserve it

Comments

Comments must be timeless — no references to this conversation, refactoring history, or the AI.

Patterns used in this codebase:

• /** JSDoc */ — file headers (after license) and exported functions/interfaces
• // N. Description — numbered sequential steps inside function bodies. Use when a function has 3+ distinct phases where at least one isn't immediately obvious from the code. Each step marks the start of a logical phase. Reference: AgentExecutionService.execute (steps 1-9) and injectModelIntoReport (steps 1-5)
• // === Section === — high-level dividers between groups of functions in long files, or to label major branching/classification blocks (e.g., // === SPENDING CAP SAFEGUARD ===). Not for sequential steps inside function bodies — use numbered steps for that
• // NOTE: / // WARNING: / // IMPORTANT: — gotchas and constraints

Never: obvious comments, conversation references ("as discussed"), history ("moved from X")

Key Files

CLI: shannon (entry point), apps/cli/src/index.ts (dispatcher), apps/cli/src/docker.ts (orchestration), apps/cli/src/mode.ts (auto-detection)

Entry Points: apps/worker/src/temporal/workflows.ts, apps/worker/src/temporal/activities.ts, apps/worker/src/temporal/worker.ts

Core Logic: apps/worker/src/session-manager.ts, apps/worker/src/ai/pi/pi-executor.ts, apps/worker/src/ai/pi/permission-system.ts (writes code_path deny rules to the @gotgenes/pi-permission-system global config), apps/worker/src/config-parser.ts, apps/worker/src/services/ (incl. preflight.ts, findings-renderer.ts, reporting.ts), apps/worker/src/audit/

Config: docker-compose.yml, apps/cli/infra/compose.yml, apps/worker/configs/, apps/worker/prompts/, tsconfig.base.json (shared compiler options), turbo.json, biome.json

CI/CD: .github/workflows/release.yml (Docker Hub push + npm publish + GitHub release, manual dispatch)

Package Installation

Package managers are configured with a minimum release age (7 days). Requires pnpm >= 10.16.0. If pnpm install fails due to a package being too new, do not attempt to bypass it — report the blocked package to the user and stop.

Troubleshooting

• "Repository not found" — Pass a bare name (-r my-repo) for ./repos/my-repo, or a path (-r /path/to/repo) for any directory
• "Temporal not ready" — Wait for health check or docker compose logs temporal
• Worker not processing — Check docker ps --filter "name=shannon-worker-"
• Reset state — ./shannon stop --clean
• Local apps unreachable — Use host.docker.internal instead of localhost
• Container permissions — On Linux, may need sudo for docker commands