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/monitor_mamba2_hyperopt.sh

@@ -0,0 +1,47 @@
+#!/bin/bash
+# Monitor MAMBA2 Hyperopt Results on Runpod S3
+
+ENDPOINT="https://s3api-eur-is-1.runpod.io"
+PROFILE="runpod"
+BUCKET="s3://se3zdnb5o4"
+
+echo "╔════════════════════════════════════════════════════════════════════╗"
+echo "║  MAMBA2 Hyperopt Results Monitor                                  ║"
+echo "╚════════════════════════════════════════════════════════════════════╝"
+echo ""
+
+# Check if results directory exists
+echo "Checking S3 for hyperopt results..."
+echo ""
+
+aws s3 ls ${BUCKET}/results/ \
+  --profile ${PROFILE} \
+  --endpoint-url ${ENDPOINT} \
+  --human-readable \
+  --recursive 2>/dev/null
+
+if [ $? -eq 0 ]; then
+  echo ""
+  echo "To download best parameters:"
+  echo ""
+  echo "  aws s3 cp ${BUCKET}/results/mamba2_13param_best_params_*.json \\"
+  echo "    /tmp/mamba2_best_params.json \\"
+  echo "    --profile ${PROFILE} \\"
+  echo "    --endpoint-url ${ENDPOINT}"
+  echo ""
+  echo "To download full log:"
+  echo ""
+  echo "  aws s3 cp ${BUCKET}/results/mamba2_13param_hyperopt_*.log \\"
+  echo "    /tmp/mamba2_hyperopt.log \\"
+  echo "    --profile ${PROFILE} \\"
+  echo "    --endpoint-url ${ENDPOINT}"
+  echo ""
+else
+  echo ""
+  echo "No results found yet. Hyperopt is likely still running."
+  echo ""
+  echo "Expected completion time: 60-90 minutes from deployment"
+  echo ""
+  echo "Run this script again in 10-15 minutes to check progress."
+  echo ""
+fi