refactor: consolidate file layout and break circular dependencies

- Move error-handling, git-manager, prompt-manager, queue-validation, and reporting into src/services/
- Delete src/constants.ts — relocate AGENT_VALIDATORS and MCP_AGENT_MAPPING into session-manager.ts alongside agent definitions
- Delete src/utils/output-formatter.ts — absorb filterJsonToolCalls and getAgentPrefix into ai/output-formatters.ts
- Extract ActivityLogger interface into src/types/activity-logger.ts to break temporal/ → services circular dependency
- Consolidate VulnType, ExploitationDecision into types/agents.ts and SessionMetadata into types/audit.ts
- Remove dead timingResults/costResults globals from utils/metrics.ts and all consumers

src/audit/audit-session.ts

@@ -18,7 +18,7 @@ import { initializeAuditStructure, type SessionMetadata } from './utils.js';
 import { formatTimestamp } from '../utils/formatting.js';
 import { SessionMutex } from '../utils/concurrency.js';
 import type { AgentEndResult } from '../types/index.js';
-import { PentestError } from '../error-handling.js';
+import { PentestError } from '../services/error-handling.js';
 import { ErrorCode } from '../types/errors.js';
 
 // Global mutex instance

src/audit/metrics-tracker.ts

@@ -18,7 +18,7 @@ import {
 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 { PentestError } from '../error-handling.js';
+import { PentestError } from '../services/error-handling.js';
 import { ErrorCode } from '../types/errors.js';
 import type { AgentName, AgentEndResult } from '../types/index.js';
 

src/audit/utils.ts

@@ -15,9 +15,10 @@ import fs from 'fs/promises';
 import path from 'path';
 import { fileURLToPath } from 'url';
 
-// Import and re-export file I/O utilities from canonical location
-import { ensureDirectory, atomicWrite, readJson, fileExists } from '../utils/file-io.js';
-export { ensureDirectory, atomicWrite, readJson, fileExists };
+import { ensureDirectory } from '../utils/file-io.js';
+
+export type { SessionMetadata } from '../types/audit.js';
+import type { SessionMetadata } from '../types/audit.js';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -26,14 +27,6 @@ const __dirname = path.dirname(__filename);
 const SHANNON_ROOT = path.resolve(__dirname, '..', '..');
 const AUDIT_LOGS_DIR = path.join(SHANNON_ROOT, 'audit-logs');
 
-export interface SessionMetadata {
-  id: string;
-  webUrl: string;
-  repoPath?: string;
-  outputPath?: string;
-  [key: string]: unknown;
-}
-
 /**
  * Extract and sanitize hostname from URL for use in identifiers
  */