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/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';