feat: implement unified audit system v3.0 with crash-safety and self-healing

## Unified Audit System (v3.0)
- Implemented crash-safe, append-only logging to audit-logs/{hostname}_{sessionId}/
- Added session.json with comprehensive metrics (timing, cost, attempts)
- Agent execution logs with turn-by-turn detail
- Prompt snapshots saved to audit-logs/.../prompts/{agent}.md
- SessionMutex prevents race conditions during parallel execution
- Self-healing reconciliation before every CLI command

## Session Metadata Standardization
- Fixed critical bug: standardized on 'id' field (not 'sessionId') throughout codebase
- Updated: shannon.mjs (recon, report), src/phases/pre-recon.js
- Added validation in AuditSession to fail fast on incorrect field usage
- JavaScript shorthand syntax was causing wrong field names

## Schema Improvements
- session.json: Added cost_usd per phase, removed redundant final_cost_usd
- Renamed 'percentage' -> 'duration_percentage' for clarity
- Simplified agent metrics to single total_cost_usd field
- Removed unused validation object from schema

## Legacy System Removal
- Removed savePromptSnapshot() - prompts now only saved by audit system
- Removed target repo pollution (prompt-snapshots/ no longer created)
- Single source of truth: audit-logs/{hostname}_{sessionId}/prompts/

## Export Script Simplification
- Removed JSON export mode (session.json already exists)
- CSV-only export with clean columns: agent, phase, status, attempts, duration_ms, cost_usd
- Tested on real session data

## Documentation
- Updated CLAUDE.md with audit system architecture
- Added .gitignore entry for audit-logs/

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/checkpoint-manager.js

@@ -79,7 +79,7 @@ const rollbackGitToCommit = async (targetRepo, commitHash) => {
 export const runSingleAgent = async (agentName, session, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt, allowRerun = false, skipWorkspaceClean = false) => {
   // Validate agent first
   const agent = validateAgent(agentName);
-  
+
   console.log(chalk.cyan(`\n🤖 Running agent: ${agent.displayName}`));
   
   // Reload session to get latest state (important for agent ranges)
@@ -191,7 +191,7 @@ export const runSingleAgent = async (agentName, session, pipelineTestingMode, ru
       AGENTS[agentName].displayName,
       agentName,  // Pass agent name for snapshot creation
       getAgentColor(agentName),  // Pass color function for this agent
-      { webUrl: session.webUrl, sessionId: session.id }  // Session metadata for logging
+      { id: session.id, webUrl: session.webUrl, repoPath: session.repoPath }  // Session metadata for audit logging
     );
     
     if (!result.success) {
@@ -616,13 +616,35 @@ export const rollbackTo = async (targetAgent, session) => {
   }
   
   const commitHash = session.checkpoints[targetAgent];
-  
+
   // Rollback git workspace
   await rollbackGitToCommit(session.targetRepo, commitHash);
-  
-  // Update session state
+
+  // Update session state (removes agents from completedAgents)
   await rollbackToAgent(session.id, targetAgent);
-  
+
+  // Mark rolled-back agents in audit system (for forensic trail)
+  try {
+    const { AuditSession } = await import('./audit/index.js');
+    const auditSession = new AuditSession(session);
+    await auditSession.initialize();
+
+    // Find agents that were rolled back (agents after targetAgent)
+    const targetOrder = AGENTS[targetAgent].order;
+    const rolledBackAgents = Object.values(AGENTS)
+      .filter(agent => agent.order > targetOrder)
+      .map(agent => agent.name);
+
+    // Mark them as rolled-back in audit system
+    if (rolledBackAgents.length > 0) {
+      await auditSession.markMultipleRolledBack(rolledBackAgents);
+      console.log(chalk.gray(`   Marked ${rolledBackAgents.length} agents as rolled-back in audit logs`));
+    }
+  } catch (error) {
+    // Non-critical: rollback succeeded even if audit update failed
+    console.log(chalk.yellow(`   ⚠️ Failed to update audit logs: ${error.message}`));
+  }
+
   console.log(chalk.green(`✅ Successfully rolled back to agent '${targetAgent}'`));
 };