chore: remove reconcile-session.js script

Reasoning:
- Shannon is a local CLI tool with direct filesystem access
- Manual file editing (JSON, rm -rf) is simpler than reconciliation script
- Automatic reconciliation runs before every command (built-in)
- If auto-reconciliation has bugs, fix the code, don't create workarounds
- Over-engineered for a local development tool

For recovery: Just delete .shannon-store.json or edit JSON files directly

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

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

CLAUDE.md

@@ -223,8 +223,7 @@ The agent implements a crash-safe, self-healing audit system (v3.0) with the fol
 - Safe parallel execution of vulnerability and exploitation phases
 
 **Metrics & Reporting:**
-- Export metrics with `./scripts/export-metrics.js`
-- Manual reconciliation (diagnostics) with `./scripts/reconcile-session.js`
+- Export metrics to CSV with `./scripts/export-metrics.js`
 - Phase-level and agent-level timing/cost aggregations
 - Validation results integrated with metrics
 
@@ -306,8 +305,7 @@ login_resources/                 # Authentication utilities
 ├── generate-totp.mjs            # TOTP generation
 └── login_instructions.txt       # Login documentation
 scripts/                         # Utility scripts
-├── reconcile-session.js         # Manual reconciliation (diagnostics)
-└── export-metrics.js            # Export metrics to CSV/JSON
+└── export-metrics.js            # Export metrics to CSV
 deliverables/                    # Output directory (in target repo)
 docs/                            # Documentation
 ├── unified-audit-system-design.md
@@ -331,14 +329,8 @@ Missing tools can be skipped using `--pipeline-testing` mode during development:
 
 ### Diagnostic & Utility Scripts
 ```bash
-# Manual reconciliation (for diagnostics only)
-./scripts/reconcile-session.js --session-id <id> --dry-run --verbose
-
-# Export metrics to CSV/JSON
-./scripts/export-metrics.js --session-id <id> --format csv --output metrics.csv
-
-# System-wide consistency audit
-./scripts/reconcile-session.js --all-sessions --dry-run
+# Export metrics to CSV
+./scripts/export-metrics.js --session-id <id> --output metrics.csv
 ```
 
-Note: Manual reconciliation should rarely be needed. Frequent use indicates bugs in automatic reconciliation.
+Note: For recovery from corrupted state, simply delete `.shannon-store.json` or edit JSON files directly.

scripts/reconcile-session.js

@@ -1,225 +0,0 @@
-#!/usr/bin/env node
-
-/**
- * Manual Session Reconciliation Script
- *
- * Purpose: Diagnostics and exceptional recovery (NOT normal operations).
- *
- * Use Cases:
- * 1. Diagnostics (Primary): Non-destructively report inconsistencies
- * 2. Debugging: Test reconciliation logic in isolation
- * 3. Exceptional Recovery: Malformed JSON recovery, reconciliation bugs
- * 4. Bulk Operations: System-wide consistency audit
- *
- * Design Principle:
- * "Self-healing is the norm. Manual intervention is the exception."
- *
- * Red Flags (indicate bugs):
- * - Manual script needed frequently
- * - Automatic reconciliation failing consistently
- * - Manual intervention after every crash
- */
-
-import chalk from 'chalk';
-import { fs, path } from 'zx';
-import { reconcileSession, getSession } from '../src/session-manager.js';
-
-const STORE_FILE = path.join(process.cwd(), '.shannon-store.json');
-
-// Parse command-line arguments
-function parseArgs() {
-  const args = {
-    sessionId: null,
-    allSessions: false,
-    dryRun: false,
-    verbose: false
-  };
-
-  for (let i = 2; i < process.argv.length; i++) {
-    const arg = process.argv[i];
-
-    if (arg === '--session-id' && process.argv[i + 1]) {
-      args.sessionId = process.argv[i + 1];
-      i++;
-    } else if (arg === '--all-sessions') {
-      args.allSessions = true;
-    } else if (arg === '--dry-run') {
-      args.dryRun = true;
-    } else if (arg === '--verbose') {
-      args.verbose = true;
-    } else if (arg === '--help' || arg === '-h') {
-      printUsage();
-      process.exit(0);
-    } else {
-      console.log(chalk.red(`❌ Unknown argument: ${arg}`));
-      printUsage();
-      process.exit(1);
-    }
-  }
-
-  return args;
-}
-
-function printUsage() {
-  console.log(chalk.cyan('\n📋 Manual Session Reconciliation Script'));
-  console.log(chalk.gray('\nUsage: ./scripts/reconcile-session.js [options]\n'));
-  console.log(chalk.white('Options:'));
-  console.log(chalk.gray('  --session-id <id>      Reconcile specific session'));
-  console.log(chalk.gray('  --all-sessions         Reconcile all sessions'));
-  console.log(chalk.gray('  --dry-run              Report inconsistencies without fixing'));
-  console.log(chalk.gray('  --verbose              Detailed logging'));
-  console.log(chalk.gray('  --help, -h             Show this help\n'));
-  console.log(chalk.white('Examples:'));
-  console.log(chalk.gray('  # Diagnostics (primary use case)'));
-  console.log(chalk.gray('  ./scripts/reconcile-session.js --session-id abc123 --dry-run\n'));
-  console.log(chalk.gray('  # System-wide consistency audit'));
-  console.log(chalk.gray('  ./scripts/reconcile-session.js --all-sessions --dry-run --verbose\n'));
-  console.log(chalk.gray('  # Exceptional recovery'));
-  console.log(chalk.gray('  ./scripts/reconcile-session.js --session-id abc123\n'));
-}
-
-// Load all sessions
-async function loadAllSessions() {
-  try {
-    if (!await fs.pathExists(STORE_FILE)) {
-      return [];
-    }
-
-    const content = await fs.readFile(STORE_FILE, 'utf8');
-    const store = JSON.parse(content);
-    return Object.values(store.sessions || {});
-  } catch (error) {
-    throw new Error(`Failed to load sessions: ${error.message}`);
-  }
-}
-
-// Reconcile a single session
-async function reconcileSingleSession(sessionId, dryRun, verbose) {
-  try {
-    const session = await getSession(sessionId);
-    if (!session) {
-      console.log(chalk.red(`❌ Session ${sessionId} not found`));
-      return { success: false, sessionId };
-    }
-
-    if (verbose) {
-      console.log(chalk.blue(`\n🔍 Analyzing session: ${sessionId}`));
-      console.log(chalk.gray(`   Web URL: ${session.webUrl}`));
-      console.log(chalk.gray(`   Status: ${session.status}`));
-      console.log(chalk.gray(`   Completed Agents: ${session.completedAgents.length}`));
-    }
-
-    if (dryRun) {
-      console.log(chalk.yellow(`   [DRY RUN] Would reconcile session ${sessionId.substring(0, 8)}...`));
-      return { success: true, sessionId, dryRun: true };
-    }
-
-    // Perform actual reconciliation
-    const report = await reconcileSession(sessionId);
-
-    const hasChanges = report.promotions.length > 0 ||
-                       report.demotions.length > 0 ||
-                       report.failures.length > 0;
-
-    if (hasChanges) {
-      console.log(chalk.green(`✅ Reconciled session ${sessionId.substring(0, 8)}...`));
-
-      if (report.promotions.length > 0) {
-        console.log(chalk.blue(`   ➕ Added ${report.promotions.length} completed agents: ${report.promotions.join(', ')}`));
-      }
-      if (report.demotions.length > 0) {
-        console.log(chalk.yellow(`   ➖ Removed ${report.demotions.length} rolled-back agents: ${report.demotions.join(', ')}`));
-      }
-      if (report.failures.length > 0) {
-        console.log(chalk.red(`   ❌ Marked ${report.failures.length} failed agents: ${report.failures.join(', ')}`));
-      }
-    } else {
-      if (verbose) {
-        console.log(chalk.gray(`   ✓ No inconsistencies found`));
-      }
-    }
-
-    return { success: true, sessionId, ...report };
-  } catch (error) {
-    console.log(chalk.red(`❌ Failed to reconcile session ${sessionId}: ${error.message}`));
-    return { success: false, sessionId, error: error.message };
-  }
-}
-
-// Main execution
-async function main() {
-  const args = parseArgs();
-
-  console.log(chalk.cyan.bold('\n🔄 Manual Session Reconciliation\n'));
-
-  if (args.dryRun) {
-    console.log(chalk.yellow('⚠️  DRY RUN MODE - No changes will be made\n'));
-  }
-
-  let sessions = [];
-
-  if (args.sessionId) {
-    sessions = [{ id: args.sessionId }];
-  } else if (args.allSessions) {
-    sessions = await loadAllSessions();
-    console.log(chalk.blue(`Found ${sessions.length} sessions\n`));
-  } else {
-    console.log(chalk.red('❌ Must specify either --session-id or --all-sessions'));
-    printUsage();
-    process.exit(1);
-  }
-
-  const results = {
-    total: sessions.length,
-    success: 0,
-    failed: 0,
-    totalPromotions: 0,
-    totalDemotions: 0,
-    totalFailures: 0
-  };
-
-  for (const session of sessions) {
-    const result = await reconcileSingleSession(session.id, args.dryRun, args.verbose);
-
-    if (result.success) {
-      results.success++;
-      results.totalPromotions += result.promotions?.length || 0;
-      results.totalDemotions += result.demotions?.length || 0;
-      results.totalFailures += result.failures?.length || 0;
-    } else {
-      results.failed++;
-    }
-  }
-
-  // Summary
-  console.log(chalk.cyan.bold('\n📊 Summary:'));
-  console.log(chalk.gray(`Total sessions: ${results.total}`));
-  console.log(chalk.green(`Successful: ${results.success}`));
-  if (results.failed > 0) {
-    console.log(chalk.red(`Failed: ${results.failed}`));
-  }
-  console.log(chalk.blue(`Promotions: ${results.totalPromotions}`));
-  console.log(chalk.yellow(`Demotions: ${results.totalDemotions}`));
-  console.log(chalk.red(`Failures: ${results.totalFailures}`));
-
-  // Health check
-  if (args.allSessions) {
-    const consistencyRate = (results.success / results.total) * 100;
-    console.log(chalk.cyan(`\n📈 Consistency Rate: ${consistencyRate.toFixed(1)}%`));
-
-    if (consistencyRate < 98) {
-      console.log(chalk.red('\n⚠️  WARNING: Low consistency rate detected!'));
-      console.log(chalk.red('This may indicate bugs in automatic reconciliation.'));
-    }
-  }
-
-  console.log();
-}
-
-main().catch(error => {
-  console.log(chalk.red.bold(`\n🚨 Fatal error: ${error.message}`));
-  if (process.env.DEBUG) {
-    console.log(chalk.gray(error.stack));
-  }
-  process.exit(1);
-});