Slot 28 RepoQA large-repo tasks into wave 2 first

Split wave2_both.json (75 tasks) into:
- wave2_repoqa.json (28 tasks): 14 ccb_understand + 14 ccb_mcp_onboarding
  RepoQA search tasks that have never been run with Haiku
- wave2_remainder.json (47 tasks): original variance rerun tasks

Wave runner now executes RepoQA first in wave 2, then remainder.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sjarmak

configs/run_variance_waves.sh

@@ -0,0 +1,108 @@
+#!/bin/bash
+# Run all variance rerun waves sequentially (designed for overnight unattended execution).
+# Each wave adds 1 run per task toward the target of 3 runs per config.
+#
+# Usage:
+#   nohup ./configs/run_variance_waves.sh > logs/variance_waves_$(date +%Y%m%d_%H%M%S).log 2>&1 &
+#
+# To start from a specific wave (e.g., after wave 1 already ran):
+#   nohup ./configs/run_variance_waves.sh --start-wave 2 > logs/variance_waves_$(date +%Y%m%d_%H%M%S).log 2>&1 &
+
+set -e
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$SCRIPT_DIR/.."
+cd "$REPO_ROOT"
+
+START_STEP=1
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --start-step) START_STEP="$2"; shift 2 ;;
+        *) echo "Unknown option: $1"; exit 1 ;;
+    esac
+done
+
+WAVE_DIR="configs/variance_reruns"
+RUNNER="./configs/run_selected_tasks.sh"
+LOG_DIR="logs"
+mkdir -p "$LOG_DIR"
+
+STARTED_AT=$(date '+%Y-%m-%d %H:%M:%S')
+echo "=============================================="
+echo "Variance Rerun — All Waves"
+echo "=============================================="
+echo "Started:     $STARTED_AT"
+echo "Start step:  $START_STEP"
+echo ""
+
+# Each entry: wave_num selection_file flags
+STEPS=(
+    "1 wave1_both.json "
+    "1 wave1_baseline_only.json --baseline-only"
+    "1 wave1_mcp_only.json --full-only"
+    "2 wave2_repoqa.json "
+    "2 wave2_remainder.json "
+    "2 wave2_baseline_only.json --baseline-only"
+    "2 wave2_mcp_only.json --full-only"
+    "3 wave3_both.json "
+    "3 wave3_baseline_only.json --baseline-only"
+)
+
+TOTAL=${#STEPS[@]}
+STEP_NUM=0
+FAILED=0
+
+for entry in "${STEPS[@]}"; do
+    read -r wave_num selection_file flags <<< "$entry"
+    STEP_NUM=$((STEP_NUM + 1))
+
+    # Skip steps below start
+    if [ "$STEP_NUM" -lt "$START_STEP" ]; then
+        echo "[Step $STEP_NUM/$TOTAL] SKIP (step $STEP_NUM < start_step $START_STEP)"
+        continue
+    fi
+
+    selection_path="${WAVE_DIR}/${selection_file}"
+    if [ ! -f "$selection_path" ]; then
+        echo "[Step $STEP_NUM/$TOTAL] SKIP — $selection_path not found"
+        continue
+    fi
+
+    # Check if selection file has any tasks
+    task_count=$(python3 -c "import json; print(len(json.load(open('$selection_path')).get('tasks',[])))")
+    if [ "$task_count" -eq 0 ]; then
+        echo "[Step $STEP_NUM/$TOTAL] SKIP — $selection_file has 0 tasks"
+        continue
+    fi
+
+    step_log="${LOG_DIR}/wave${wave_num}_${selection_file%.json}_$(date +%Y%m%d_%H%M%S).log"
+
+    echo ""
+    echo "=============================================="
+    echo "[Step $STEP_NUM/$TOTAL] Wave $wave_num — $selection_file ($task_count tasks) $flags"
+    echo "  Log: $step_log"
+    echo "  Started: $(date '+%Y-%m-%d %H:%M:%S')"
+    echo "=============================================="
+
+    # Pipe newline to auto-confirm the interactive prompt.
+    # Tee to both step log and stdout so the wrapper log captures everything.
+    if echo "" | $RUNNER \
+        --selection-file "$selection_path" \
+        --category staging \
+        $flags \
+        2>&1 | tee "$step_log"; then
+        echo "[Step $STEP_NUM/$TOTAL] DONE at $(date '+%Y-%m-%d %H:%M:%S')"
+    else
+        echo "[Step $STEP_NUM/$TOTAL] FAILED (exit $?) at $(date '+%Y-%m-%d %H:%M:%S')"
+        FAILED=$((FAILED + 1))
+        # Continue to next step — don't abort the whole overnight run
+    fi
+done
+
+echo ""
+echo "=============================================="
+echo "All waves complete"
+echo "  Started:  $STARTED_AT"
+echo "  Finished: $(date '+%Y-%m-%d %H:%M:%S')"
+echo "  Failed steps: $FAILED / $TOTAL"
+echo "=============================================="