chore: Second cleanup wave - organize root directory

- Archive: 85 agent .txt files → docs/archive/agents/legacy_txt/
- Scripts: Move 110 shell scripts → scripts/ (keep deploy.sh in root)
- Models: Move 18 .safetensors → ml/models/checkpoints/training_artifacts/
- Delete: 34 directories (~33GB freed) - target/, coverage_*, test artifacts
- Build: Clean 14 build artifacts (.rlib, .o, .pid, binaries)
- Tests: Move 14 .rs files → tests/standalone/
- SQL: Move 5 files → sql/ (keep init-db*.sql for Docker)
- Wave 153: Archive to docs/archive/historical/wave153/
- Docs: Archive 9 markdown files to wave_d/reports/ and historical/

Total impact: ~34GB freed (both waves), root directory cleaned from 583 to ~40 essential files
Directory count reduced from 65 to 31 (52% reduction)
All historical data preserved in organized archive structure

scripts/optimize_batch_sizes.sh

@@ -0,0 +1,101 @@
+#!/bin/bash
+# GPU Batch Size Optimization Script for RTX 3050 Ti (4GB VRAM)
+#
+# Tests optimal batch sizes for TFT, MAMBA-2, and Liquid models
+# Generates BATCH_SIZE_OPTIMIZATION_REPORT.md with recommendations
+
+set -e
+
+echo "==================================="
+echo "GPU Batch Size Optimization"
+echo "==================================="
+echo ""
+
+# Check if nvidia-smi is available
+if ! command -v nvidia-smi &> /dev/null; then
+    echo "ERROR: nvidia-smi not found. This script requires NVIDIA GPU."
+    exit 1
+fi
+
+# Display GPU info
+echo "GPU Information:"
+nvidia-smi --query-gpu=name,memory.total,driver_version --format=csv,noheader
+echo ""
+
+# Check CUDA availability
+echo "Checking CUDA setup..."
+if [ -d "/usr/local/cuda" ]; then
+    echo "✓ CUDA found at /usr/local/cuda"
+    nvcc --version | head -n 1
+else
+    echo "⚠ CUDA not found at /usr/local/cuda (will fall back to CPU)"
+fi
+echo ""
+
+# Build the optimization tool in release mode
+echo "Building optimization tool (release mode)..."
+cargo build -p ml --example optimize_batch_sizes --release
+
+if [ $? -ne 0 ]; then
+    echo "ERROR: Failed to build optimization tool"
+    exit 1
+fi
+
+echo "✓ Build complete"
+echo ""
+
+# Run the optimization
+echo "Running batch size optimization..."
+echo "This will test:"
+echo "  - TFT: batch sizes [16, 32, 64, 128]"
+echo "  - MAMBA-2: batch sizes [8, 16, 32]"
+echo "  - Liquid: batch sizes [16, 32, 64]"
+echo ""
+echo "Estimated runtime: 3-5 minutes"
+echo ""
+
+# Monitor VRAM usage in background
+echo "Starting VRAM monitor..."
+(
+    while true; do
+        nvidia-smi --query-gpu=memory.used,memory.total --format=csv,noheader,nounits | \
+        awk '{printf "VRAM: %d MB / %d MB (%.1f%%)\r", $1, $2, ($1/$2)*100}'
+        sleep 1
+    done
+) &
+MONITOR_PID=$!
+
+# Run the optimization
+cargo run -p ml --example optimize_batch_sizes --release
+
+# Kill the monitor
+kill $MONITOR_PID 2>/dev/null || true
+echo ""
+
+# Check if report was generated
+if [ -f "BATCH_SIZE_OPTIMIZATION_REPORT.md" ]; then
+    echo ""
+    echo "==================================="
+    echo "Optimization Complete!"
+    echo "==================================="
+    echo ""
+    echo "Report generated: BATCH_SIZE_OPTIMIZATION_REPORT.md"
+    echo ""
+
+    # Extract recommendations
+    echo "Recommended Batch Sizes:"
+    grep -A 10 "## Optimization Summary" BATCH_SIZE_OPTIMIZATION_REPORT.md | \
+    grep -E "^\| (TFT|MAMBA-2|Liquid)" | \
+    awk -F'|' '{print "  " $2 " -> batch_size = " $3}' | \
+    sed 's/  //' | sed 's/^ *//'
+
+    echo ""
+    echo "Next Steps:"
+    echo "1. Review BATCH_SIZE_OPTIMIZATION_REPORT.md for detailed results"
+    echo "2. Update model configurations with recommended batch sizes"
+    echo "3. Test training with optimized batch sizes"
+else
+    echo ""
+    echo "ERROR: Report not generated"
+    exit 1
+fi