commit-changes.sh

#!/bin/bash
# Stage and commit all thermodynamic architecture changes
# Run from repo root: bash commit-changes.sh

set -e

echo "🚀 Starting git staging and commit process..."
echo ""

# Step 1: Check git status
echo "📋 Current git status:"
git status --short
echo ""

# Step 2: Stage all changes
echo "📝 Staging all changes..."
git add .
echo "✅ All files staged"
echo ""

# Step 3: Show what will be committed
echo "📊 Files to be committed:"
git diff --cached --name-only
echo ""

# Step 4: Commit
echo "💾 Creating commit..."
git commit -m "feat: implement thermodynamic architecture & fix CVEs

Implements Active Subject Matrix system with automatic configuration 
shift detection and phase continuity preservation.

Features:
- Add semantic routing (Navigator → subject_a, activeFocus → subject_b)
- Implement configuration shift detection and formatting
- Add React hook for matrix state management
- Add intent-based doctrine loading (CHAT vs READ modes)
- Support mode transitions: chat ↔ solo ↔ dyad ↔ observer

Security:
- Upgrade Next.js 16.1.1 → 16.1.5
- Fix CVE-2025-59471 (DoS Image Optimizer)
- Fix CVE-2025-59472 (PPR memory exhaustion)
- Fix GHSA-h25m-26qc-wcjf (HTTP request DoS)

Documentation:
- Add formal architecture specification
- Add integration guide with examples
- Add configuration shift utilities
- Add test suite for shift detection

Breaking Changes: None (backward compatible)"

echo ""
echo "✅ Commit successful!"
echo ""

# Step 5: Install new dependencies
echo "📦 Installing updated dependencies..."
cd vessel
npm install
echo "✅ Dependencies installed"
echo ""

# Step 6: Verify build
echo "🔨 Verifying TypeScript build..."
npm run build
echo "✅ Build successful"
echo ""

echo "🎉 All done! Your changes have been committed and built successfully."
echo ""
echo "Next steps:"
echo "1. Run 'npm run dev' to test locally"
echo "2. See INTEGRATION_GUIDE_ACTIVE_SUBJECT_MATRIX.md for next phases"