Feat/temporal (#46)

* refactor: modularize claude-executor and extract shared utilities

- Extract message handling into src/ai/message-handlers.ts with pure functions
- Extract output formatting into src/ai/output-formatters.ts
- Extract progress management into src/ai/progress-manager.ts
- Add audit-logger.ts with Null Object pattern for optional logging
- Add shared utilities: formatting.ts, file-io.ts, functional.ts
- Consolidate getPromptNameForAgent into src/types/agents.ts

* feat: add Claude Code custom commands for debug and review

* feat: add Temporal integration foundation (phase 1-2)

- Add Temporal SDK dependencies (@temporalio/client, worker, workflow, activity)
- Add shared types for pipeline state, metrics, and progress queries
- Add classifyErrorForTemporal() for retry behavior classification
- Add docker-compose for Temporal server with SQLite persistence

* feat: add Temporal activities for agent execution (phase 3)

- Add activities.ts with heartbeat loop, git checkpoint/rollback, and error classification
- Export runClaudePrompt, validateAgentOutput, ClaudePromptResult for Temporal use
- Track attempt number via Temporal Context for accurate audit logging
- Rollback git workspace before retry to ensure clean state

* feat: add Temporal workflow for 5-phase pipeline orchestration (phase 4)

* feat: add Temporal worker, client, and query tools (phase 5)

- Add worker.ts with workflow bundling and graceful shutdown
- Add client.ts CLI to start pipelines with progress polling
- Add query.ts CLI to inspect running workflow state
- Fix buffer overflow by truncating error messages and stack traces
- Skip git operations gracefully on non-git repositories
- Add kill.sh/start.sh dev scripts and Dockerfile.worker

* feat: fix Docker worker container setup

- Install uv instead of deprecated uvx package
- Add mcp-server and configs directories to container
- Mount target repo dynamically via TARGET_REPO env variable

* fix: add report assembly step to Temporal workflow

- Add assembleReportActivity to concatenate exploitation evidence files before report agent runs
- Call assembleFinalReport in workflow Phase 5 before runReportAgent
- Ensure deliverables directory exists before writing final report
- Simplify pipeline-testing report prompt to just prepend header

* refactor: consolidate Docker setup to root docker-compose.yml

* feat: improve Temporal client UX and env handling

- Change default to fire-and-forget (--wait flag to opt-in)
- Add splash screen and improve console output formatting
- Add .env to gitignore, remove from dockerignore for container access
- Add Taskfile for common development commands

* refactor: simplify session ID handling and improve Taskfile options

- Include hostname in workflow ID for better audit log organization
- Extract sanitizeHostname utility to audit/utils.ts for reuse
- Remove unused generateSessionLogPath and buildLogFilePath functions
- Simplify Taskfile with CONFIG/OUTPUT/CLEAN named parameters

* chore: add .env.example and simplify .gitignore

* docs: update README and CLAUDE.md for Temporal workflow usage

- Replace Docker CLI instructions with Task-based commands
- Add monitoring/stopping sections and workflow examples
- Document Temporal orchestration layer and troubleshooting
- Simplify file structure to key files overview

* refactor: replace Taskfile with bash CLI script

- Add shannon bash script with start/logs/query/stop/help commands
- Remove Taskfile.yml dependency (no longer requires Task installation)
- Update README.md and CLAUDE.md to use ./shannon commands
- Update client.ts output to show ./shannon commands

* docs: fix deliverable filename in README

* refactor: remove direct CLI and .shannon-store.json in favor of Temporal

- Delete src/shannon.ts direct CLI entry point (Temporal is now the only mode)
- Remove .shannon-store.json session lock (Temporal handles workflow deduplication)
- Remove broken scripts/export-metrics.js (imported non-existent function)
- Update package.json to remove main, start script, and bin entry
- Clean up CLAUDE.md and debug.md to remove obsolete references

* chore: remove licensing comments from prompt files to prevent leaking into actual prompts

* fix: resolve parallel workflow race conditions and retry logic bugs

- Fix save_deliverable race condition using closure pattern instead of global variable
- Fix error classification order so OutputValidationError matches before generic validation
- Fix ApplicationFailure re-classification bug by checking instanceof before re-throwing
- Add per-error-type retry limits (3 for output validation, 50 for billing)
- Add fast retry intervals for pipeline testing mode (10s vs 5min)
- Increase worker concurrent activities to 25 for parallel workflows

* refactor: pipeline vuln→exploit workflow for parallel execution

- Replace sync barrier between vuln/exploit phases with independent pipelines
- Each vuln type runs: vuln agent → queue check → conditional exploit
- Add checkExploitationQueue activity to skip exploits when no vulns found
- Use Promise.allSettled for graceful failure handling across pipelines
- Add PipelineSummary type for aggregated cost/duration/turns metrics

* fix: re-throw retryable errors in checkExploitationQueue

* fix: detect and retry on Claude Code spending cap errors

- Add spending cap pattern detection in detectApiError() with retryable error
- Add matching patterns to classifyErrorForTemporal() for proper Temporal retry
- Add defense-in-depth safeguard in runClaudePrompt() for $0 cost / low turn detection
- Add final sanity check in activities before declaring success

* fix: increase heartbeat timeout to prevent false worker-dead detection

Original 30s timeout was from POC spec assuming <5min activities. With
hour-long activities and multiple concurrent workflows sharing one worker,
resource contention causes event loop stalls exceeding 30s, triggering
false heartbeat timeouts. Increased to 10min (prod) and 5min (testing).

* fix: temporal db init

* fix: persist home dir

* feat: add per-workflow unified logging with ./shannon logs ID=<workflow-id>

- Add WorkflowLogger class for human-readable, per-workflow log files
- Create workflow.log in audit-logs/{workflowId}/ with phase, agent, tool, and LLM events
- Update ./shannon logs to require ID param and tail specific workflow log
- Add phase transition logging at workflow boundaries
- Include workflow completion summary with agent breakdown (duration, cost)
- Mount audit-logs volume in docker-compose for host access

---------

Co-authored-by: ezl-keygraph <ezhil@keygraph.io>

src/audit/metrics-tracker.ts

@@ -13,13 +13,12 @@
 
 import {
   generateSessionJsonPath,
-  atomicWrite,
-  readJson,
-  fileExists,
-  formatTimestamp,
-  calculatePercentage,
   type SessionMetadata,
 } from './utils.js';
+import { atomicWrite, readJson, fileExists } from '../utils/file-io.js';
+import { formatTimestamp, calculatePercentage } from '../utils/formatting.js';
+import { AGENT_PHASE_MAP, type PhaseName } from '../session-manager.js';
+import type { AgentName } from '../types/index.js';
 
 interface AttemptData {
   attempt_number: number;
@@ -152,16 +151,14 @@ export class MetricsTracker {
     }
 
     // Initialize agent metrics if not exists
-    if (!this.data.metrics.agents[agentName]) {
-      this.data.metrics.agents[agentName] = {
-        status: 'in-progress',
-        attempts: [],
-        final_duration_ms: 0,
-        total_cost_usd: 0,
-      };
-    }
-
-    const agent = this.data.metrics.agents[agentName]!;
+    const existingAgent = this.data.metrics.agents[agentName];
+    const agent = existingAgent ?? {
+      status: 'in-progress' as const,
+      attempts: [],
+      final_duration_ms: 0,
+      total_cost_usd: 0,
+    };
+    this.data.metrics.agents[agentName] = agent;
 
     // Add attempt to array
     const attempt: AttemptData = {
@@ -255,36 +252,19 @@ export class MetricsTracker {
   private calculatePhaseMetrics(
     successfulAgents: Array<[string, AgentMetrics]>
   ): Record<string, PhaseMetrics> {
-    const phases: Record<string, AgentMetrics[]> = {
+    const phases: Record<PhaseName, AgentMetrics[]> = {
       'pre-recon': [],
-      recon: [],
+      'recon': [],
       'vulnerability-analysis': [],
-      exploitation: [],
-      reporting: [],
+      'exploitation': [],
+      'reporting': [],
     };
 
-    // Map agents to phases
-    const agentPhaseMap: Record<string, string> = {
-      'pre-recon': 'pre-recon',
-      recon: 'recon',
-      'injection-vuln': 'vulnerability-analysis',
-      'xss-vuln': 'vulnerability-analysis',
-      'auth-vuln': 'vulnerability-analysis',
-      'authz-vuln': 'vulnerability-analysis',
-      'ssrf-vuln': 'vulnerability-analysis',
-      'injection-exploit': 'exploitation',
-      'xss-exploit': 'exploitation',
-      'auth-exploit': 'exploitation',
-      'authz-exploit': 'exploitation',
-      'ssrf-exploit': 'exploitation',
-      report: 'reporting',
-    };
-
-    // Group agents by phase
+    // Group agents by phase using imported AGENT_PHASE_MAP
     for (const [agentName, agentData] of successfulAgents) {
-      const phase = agentPhaseMap[agentName];
-      if (phase && phases[phase]) {
-        phases[phase]!.push(agentData);
+      const phase = AGENT_PHASE_MAP[agentName as AgentName];
+      if (phase) {
+        phases[phase].push(agentData);
       }
     }
 
@@ -296,7 +276,6 @@ export class MetricsTracker {
       if (agentList.length === 0) continue;
 
       const phaseDuration = agentList.reduce((sum, agent) => sum + agent.final_duration_ms, 0);
-
       const phaseCost = agentList.reduce((sum, agent) => sum + agent.total_cost_usd, 0);
 
       phaseMetrics[phaseName] = {