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)

# Monitor
./shannon scans                       # List running and completed scans, with each report's path
./shannon logs [<workspace>]          # Show a scan's live log (default: the single running scan, else the most recent)
./shannon logs [<workspace>] --agent <name>   # Tail one agent's own log (from .shannon/agents/)
./shannon logs [<workspace>] --list-agents    # List the agents that have their own log
./shannon status [<workspace>]        # Live phase/agent progress of one scan, read from Temporal (redraws, then exits; same default target)
# Dashboard: http://localhost:8233

# Stop
./shannon stop [<workspace>]          # Stop one scan (default: the single running scan; confirms first; --yes/-y to skip)
./shannon stop --all                  # Stop all running scans (Temporal stays up; confirms first)
./shannon reset                       # Stop everything and wipe all Temporal data + volumes (type 'confirm' to proceed; cannot be skipped)

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

# Image management
./shannon build [--no-cache]          # Local mode: build worker image

# 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), --keep-container (preserve worker container after exit for log inspection), --yes/-y (skip the confirmation prompt on stop; required for non-interactive use; reset requires a typed confirm and cannot be skipped)

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 Docker orchestration and a direct @temporalio/client integration for read-only status plus bounded workflow lifecycle operations; no worker/pipeline business logic or prompts. Bundled with tsdown for single-file ESM output (deps stay external).

• apps/cli/src/index.ts — CLI dispatcher (setup, start, stop, reset, logs, status, scans, build, version)
• apps/cli/src/temporal-client.ts — @temporalio/client integration: connects to the frontend on 127.0.0.1:7233 (published by compose), provides describeScan (status + pendingActivities → running agents), queryProgress (live getProgress query → PipelineState), getTerminalOutcome (workflow result()), and bounded lifecycle RPCs for stop. stop requests cancellation first, waits up to 10 seconds, then requests termination only when necessary and verifies closure within a bounded window. No worker of its own; scans are visible within Temporal's retention window, which ensureInfra (apps/cli/src/docker.ts) converges to 168h (7 days) on every successful shannon start; override with SHANNON_TEMPORAL_RETENTION (a positive whole-hour value like 72h)
• apps/cli/src/scan/ — status rendering: pipeline.ts (static phase/agent plan + run*Agent activity-type→agent map + mirrored PipelineState/AgentMetrics types; keep in sync with the worker), derive.ts (pure phase/agent state derivation shared by the tree and --json), render.ts (one renderer for both the live query state and the terminal result). The tree shows model work only: every row is an agent, an Agentic SAST stage, or a report step that is currently running or failed. Reconciliation is model work owned by a class, so its wall time renders as a trailing + duration on that class's exploitation row (its analysis row when exploit: false) rather than as a row of its own; deterministic bookkeeping stages (report:* renumber/assemble/finalize/surface) never appear once they complete. DerivedPhase.children (renders sub-rows) and DerivedPhase.meta (duration vs a k/N done tally) are independent — Agentic SAST lists stages under a duration, exploitation lists classes under a tally
• 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, and ephemeral docker run worker spawning. Each worker carries workspace, task-queue, and preselected workflow-ID labels so stop can correlate the local worker with its Temporal execution before session.json exists. Before docker run, start fsyncs that exact candidate under the workspace's hidden internals and clears it only when session.json registers the same ID; stop reconciles any candidate left by an interrupted launch. Start also checks the image's workflow-ID protocol label and refuses a stale worker that would ignore the preselected ID
• 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 (any absolute or 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, preselected workflow ID, matching identity labels, and isolated volume mounts. shannon stop --all takes the union of labeled running workers and Temporal-running workflows, so an orphaned workflow is still stopped after its worker has disappeared.

• 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

Around those phases:

• Optional agentic static analysis runs before the pentest when agentic_sast.enabled is "true", as a child workflow.
• After each class's analysis, reconciliation groups its findings into exploitation tasks.
• Findings outside the five classes form an internal miscellaneous class with its own exploitation agent (miscellaneous-exploit).
• A scan can finish completed, partial, failed, or cancelled; partial carries an ordered set of reasons.

Supporting Systems

• Configuration — YAML configs in apps/worker/configs/ use the closed JSON Schema in config-schema.json. Every fresh scan runs the fixed five analysis classes; there is no public class selector. agentic_sast.enabled is the only public agentic-SAST setting. Finding reconciliation runs on every scan and has no public setting of its own. Config also supports authentication (MFA/TOTP), URL/code rule scoping (rules.avoid/rules.focus), exploit, free-form rules_of_engagement, and post-hoc report options (min_severity, min_confidence, guidance, and exploit-only sarif output via apps/worker/src/services/sarif-renderer.ts, on by default for exploit runs and opt out with report.sarif: "false"). 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. Credential resolution — local mode: env vars → ./.env; npx mode: env vars → ~/.shannon/config.toml (via npx @keygraph/shannon setup)
• Agentic SAST progress — Capella runs as a child workflow, so its activities are absent from the parent's pendingActivities and invisible to the CLI. The child signals each stage boundary up via capellaStageProgress (apps/worker/src/temporal/shared.ts); the parent's handler validates the payload and writes the child-supplied startedAt and durationMs directly to operationalStages['agentic-sast:<stage>'], so both the live getProgress query and the terminal result carry per-stage rows. Signalling is best-effort and every failure is swallowed — a closed or unreachable parent must never fail a SAST run. CAPELLA_STAGE_LABELS in apps/worker/src/ai/sast/types.ts is the one label table, shared by the scan log and the status tree; CAPELLA_PROGRESS_STAGES omits export, which runs no model and so never becomes a row. Scans predating the signal keep the aggregate agentic-sast span and render as a bare phase line
• 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. Any pi-ai provider id is accepted — parseModelSpec no longer rejects against a hardcoded list, so pi's registry is the authority (an unknown provider/model surfaces as a clear "not found in pi registry" error at preflight, which points to the browsable catalogue at pi.dev/models — PI_CATALOG_URL in apps/worker/src/ai/models.ts, appended to the not-found errors and shown in the setup wizard's "Other provider" hint). Four providers are curated (CURATED_PROVIDERS: anthropic, openai, xai, amazon-bedrock) with their own credential variables, config sections, and setup flows; 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. Any other provider uses the generic credential path: SHANNON_AI_API_KEY (GENERIC_API_KEY_ENV) supplies the key for any provider whose credential is a plain API key. Curated providers' own variables take precedence over it, and it also works as a fallback for them — Bedrock is the sole exception (it authenticates through its AWS_ variables, so the generic key never stands in for it). The CLI forwards SHANNON_AI_API_KEY in COMMON_FORWARD_VARS (it is provider-neutral, binding to whatever SHANNON_AI_MODEL names, so the "only one provider configured" guard counts only named credentials), and stores it under a generic [provider] config.toml section (provider.api_key). npx @keygraph/shannon setup exposes this as the "Other provider" option: free-text provider id + model id + key (a curated provider id is rejected there, since it has its own option). SHANNON_AI_BASE_URL overrides the endpoint for any provider (proxies/gateways); the credential and API dialect are unchanged. A base URL only changes the address — resolveModel (apps/worker/src/ai/models.ts) carries it onto the model descriptor and nothing else. pi's builtin openai provider serves a single API (Responses) and dispatches on the provider rather than model.api, so an openai: gateway run always speaks Responses; a Chat-Completions-only gateway must be reached through a completions-native provider such as openrouter instead. 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
• Pi Credential Reuse — SHANNON_USE_PI_AUTH=1 opts into reusing the host's Pi login, including an openai-codex ChatGPT Plus/Pro subscription (SHANNON_AI_MODEL=openai-codex:<model-id>) or an xai Grok subscription (SHANNON_AI_MODEL=xai:<model-id>); the mechanism is provider-agnostic and works for any Pi login. apps/cli/src/env.ts requires ~/.pi/agent/auth.json; start.ts passes its path to spawnWorker, which mounts only that file read-write at /tmp/.pi/agent/auth.json. The flag itself is not forwarded: the worker detects the file with piAuthPresent() and passes its path to ModelRuntime.create. CLI and worker API-key presence checks are skipped on this path, but the normal preflight model probe still validates the credential. The image and UID-remapping entrypoint keep /tmp/.pi/agent owned by pentest so adjacent Pi/Shannon configuration remains writable. Refreshed OAuth state is persisted to the host for subsequent scans.
• Audit System — Crash-safe append-only logging in workspaces/{hostname}_{sessionId}/. The run directory's top level holds the human-facing report in both formats (Security-Assessment-Report.pdf and Security-Assessment-Report.md, FINAL_REPORT_PDF_FILENAME/FINAL_REPORT_MD_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 (scans/logs) without migration. A pre-restructure workspace cannot be resumed: classifyWorkspaceLaunch (apps/cli/src/commands/start.ts) requires .shannon/launch.json, and its absence fails the launch as "created by an earlier version of Shannon" before anything on disk is touched. There is no in-place migration — the workspace's files and report are left untouched, and the operator starts a new scan under a different -w name. The report agent writes structured findings to report.json, from which report-renderer.ts renders the assembled markdown and report-json-adapter.ts produces the Typst-shaped JSON that pdf-renderer.ts compiles into comprehensive_security_assessment_report.pdf using the bundled apps/worker/templates/typst/report.typ template (the typst binary is installed in the worker image). copyReportToRunRoot (apps/worker/src/services/reporting.ts) surfaces both the PDF and the markdown to the run root as Security-Assessment-Report.pdf and Security-Assessment-Report.md; the deliverables-dir copies remain as the git-checkpointed sources. PDF compilation is best-effort — a failure is logged and the run still completes. 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. Every combined-log line is also projected into a per-agent file under .shannon/agents/<slug>.log (one per pipeline agent, one per Capella stage; subagents fold into the parent's file, and a stage's concurrent sessions share its file with an inline session label). The projection boundary is apps/worker/src/audit/actor-projection.ts (projectActor maps a TraceActor to its combined prefix and owning file slug — slugs come only from closed fields); fan-out is best-effort and never blocks the canonical combined log. A lifecycle owner holds a LogStream lease per agent file (the pipeline agent's logAgent span, or a Capella stage activity's try/finally) so per-line writes ride the reference count; CapellaStageTrace.drain() flushes a stage's trace queue before its activity returns. The CLI tails one file with shannon logs --agent <name> (--list-agents to enumerate); the default shannon logs path is unchanged
• 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

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 path to the target repo (-r /path/to/repo or -r ./my-repo)
• "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 reset
• Local apps unreachable — Use host.docker.internal instead of localhost
• Container permissions — On Linux, may need sudo for docker commands