chore(agent-eval): add per-repo WITH-only why-Read benchmark harness

bench-why-repo.sh runs one README repo, WITH-codegraph only, N runs, each
appending a why-Read diagnostic ("if you Read/Grep, explain why codegraph fell
short; end with a ## Why I read section"). Honors EFFORT (default high) and
kills the per-repo daemon before each run so it serves the current dist. The
WITHOUT baseline is codegraph-independent and lives in the README, so it's not
re-run. Used to validate the explore reshape: all 7 README repos, 28/28 runs,
0 Read / 0 Grep on effort=high.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

scripts/agent-eval/bench-why-repo.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# One README repo, WITH-codegraph only, N runs. Each run appends a why-Read
+# diagnostic so the agent explains any Read/Grep. (The WITHOUT baseline is
+# codegraph-independent and already in the README — no point re-running it.)
+# Output -> /tmp/ab-why/<repo>/with<n>.jsonl
+# Usage: bench-why-repo.sh <repo-path> "<query>" [N]
+set -uo pipefail
+REPO="$1"; Q="$2"; N="${3:-4}"
+NAME="$(basename "$REPO")"
+CG="/Users/colby/Development/Personal/codegraph/dist/bin/codegraph.js"
+OUT="/tmp/ab-why/$NAME"; mkdir -p "$OUT"
+WHY=$'\n\nIMPORTANT — diagnostic: if you use the Read or Grep tool at ANY point, for EACH such call explain why codegraph_explore / codegraph_node did not already give you what you needed. End your entire answer with a section titled exactly "## Why I read" listing every Read and Grep you made and the precise reason codegraph fell short for it. If you used neither, write "## Why I read" then "none — codegraph was sufficient."'
+printf '{"mcpServers":{"codegraph":{"command":"%s","args":["serve","--mcp","--path","%s"]}}}' "$CG" "$REPO" > "$OUT/cg.json"
+
+for i in $(seq 1 "$N"); do
+  pkill -f "serve --mcp" 2>/dev/null; sleep 1; rm -f "$REPO/.codegraph/daemon.sock"
+  ( cd "$REPO" && claude -p "$Q$WHY" --output-format stream-json --verbose \
+      --permission-mode bypassPermissions --model opus --effort "${EFFORT:-high}" --max-budget-usd 4 \
+      --strict-mcp-config --mcp-config "$OUT/cg.json" > "$OUT/with$i.jsonl" 2>"$OUT/with$i.err" )
+  echo "WITH run $i: exit $? ($(wc -l < "$OUT/with$i.jsonl" | tr -d ' ') lines)"
+done
+echo "DONE $NAME"