fix: feat: evolve.sh auto-incrementing per-run results directory (#752)

- --output now accepts a base dir (default: evolved/) instead of requiring
  an explicit path each run
- On each invocation, scan base dir for existing run_NNN/ subdirectories,
  find the highest N, and create run_(N+1)/ for this run's outputs
- All generation JSONL files, best.push3, diff.txt, and evolution.log are
  written to the new run dir — previous runs are never overwritten
- Log header now shows both Base dir and Output (run dir) for clarity

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

tools/push3-evolution/evolve.sh

@@ -11,7 +11,7 @@
 #     --generations 5 \
 #     --mutation-rate 2 \
 #     --elites 2 \
-#     --output evolved/ \
+#     [--output evolved/] \
 #     [--diverse-seeds] \
 #     [--run-id <N>]
 #
@@ -40,7 +40,7 @@
 #   4. Show diff: original vs evolved (which constants changed, by how much).
 #
 # Output:
-#   <output>/
+#   <output>/run_NNN/        NNN auto-increments from the highest existing run dir
 #     generation_0.jsonl   {candidate_id, fitness, mutations_applied}
 #     generation_1.jsonl
 #     ...
@@ -80,7 +80,7 @@ POPULATION=10
 GENERATIONS=5
 MUTATION_RATE=2
 ELITES=2
-OUTPUT_DIR=""
+OUTPUT_DIR="evolved"
 DIVERSE_SEEDS=false
 RUN_ID=""
 
@@ -98,9 +98,8 @@ while [[ $# -gt 0 ]]; do
   esac
 done
 
-if [ -z "$SEED" ];       then echo "Error: --seed required" >&2;   exit 2; fi
-if [ -z "$OUTPUT_DIR" ]; then echo "Error: --output required" >&2; exit 2; fi
-if [ ! -f "$SEED" ];     then echo "Error: seed file not found: $SEED" >&2; exit 2; fi
+if [ -z "$SEED" ];   then echo "Error: --seed required" >&2;              exit 2; fi
+if [ ! -f "$SEED" ]; then echo "Error: seed file not found: $SEED" >&2; exit 2; fi
 
 # Validate numeric args
 for _name_val in "population:$POPULATION" "generations:$GENERATIONS" "mutation-rate:$MUTATION_RATE"; do
@@ -119,8 +118,27 @@ fi
 
 # Canonicalize paths
 SEED="$(cd "$(dirname "$SEED")" && pwd)/$(basename "$SEED")"
+
+# Resolve base output dir and create run_NNN subdirectory
+mkdir -p "$OUTPUT_DIR"
+BASE_DIR="$(cd "$OUTPUT_DIR" && pwd)"
+
+# Auto-increment: find the highest run_NNN directory under BASE_DIR and add 1
+RUN_NUM=$(python3 - "$BASE_DIR" <<'PYEOF'
+import sys, os, re
+base = sys.argv[1]
+max_n = 0
+if os.path.isdir(base):
+    for name in os.listdir(base):
+        m = re.fullmatch(r'run(\d+)', name)
+        if m and os.path.isdir(os.path.join(base, name)):
+            max_n = max(max_n, int(m.group(1)))
+print(f"{max_n + 1:03d}")
+PYEOF
+)
+
+OUTPUT_DIR="$BASE_DIR/run_${RUN_NUM}"
 mkdir -p "$OUTPUT_DIR"
-OUTPUT_DIR="$(cd "$OUTPUT_DIR" && pwd)"
 LOG="$OUTPUT_DIR/evolution.log"
 
 # Seeds pool — persistent candidate pool across all runs
@@ -294,6 +312,7 @@ log "  Mutation rate:  $MUTATION_RATE"
 log "  Elites:         $ELITES"
 log "  Diverse seeds:  $DIVERSE_SEEDS"
 log "  Run ID:         $RUN_ID"
+log "  Base dir:       $BASE_DIR"
 log "  Output:         $OUTPUT_DIR"
 log "  TSX:            $TSX_CMD"
 log "  Eval mode:      $EVAL_MODE"