chore: remove run-metadata.json functionality

Reasoning:
- Pollutes target repo with run-metadata.json
- Redundant with audit system (session.json has all metadata)
- Less useful than comprehensive audit logs
- Target repos should stay clean - only deliverables belong there

All debugging info now lives in audit-logs/{hostname}_{sessionId}/session.json

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

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

shannon.mjs

@@ -13,7 +13,6 @@ import { runPhase, getGitCommitHash } from './src/checkpoint-manager.js';
 
 // Setup and Deliverables
 import { setupLocalRepo, cleanupMCP } from './src/setup/environment.js';
-import { saveRunMetadata } from './src/setup/deliverables.js';
 
 // AI and Prompts
 import { runClaudePromptWithRetry } from './src/ai/claude-executor.js';
@@ -178,15 +177,6 @@ async function main(webUrl, repoPath, configPath = null, pipelineTestingMode = f
     );
   }
 
-  // Save run metadata with error handling
-  try {
-    await saveRunMetadata(sourceDir, webUrl, repoPath);
-  } catch (error) {
-    // Non-critical operation, log warning and continue
-    console.log(chalk.yellow(`⚠️ Failed to save run metadata: ${error.message}`));
-    await logError(error, 'Run metadata saving', sourceDir);
-  }
-
   // Check if we should continue from where session left off
   const nextAgent = getNextAgent(session);
   if (!nextAgent) {