Fix Windows smoke 14e + soak latency threshold

- Phase 14: copy binary with .exe suffix on Windows (was creating
  non-.exe copy that uninstall didn't remove)
- Phase 14e: check both .exe and non-.exe paths
- Soak latency: exclude index_repository from max query latency
  (indexing 377 files is legitimately slow on Windows/MSYS2)

Author: DeusData

scripts/smoke-test.sh

@@ -1024,10 +1024,15 @@ if [ -n "${SMOKE_DOWNLOAD_URL:-}" ]; then
   # ── 14a-f: Real update command against local HTTP server ──
   UPDATE_HOME=$(mktemp -d)
   mkdir -p "$UPDATE_HOME/.claude" "$UPDATE_HOME/.local/bin"
-  cp "$BINARY" "$UPDATE_HOME/.local/bin/codebase-memory-mcp"
-  chmod 755 "$UPDATE_HOME/.local/bin/codebase-memory-mcp"
-  if [ "$(uname -s)" = "Darwin" ]; then
-    codesign --sign - --force "$UPDATE_HOME/.local/bin/codebase-memory-mcp" 2>/dev/null || true
+  if [[ "$BINARY" == *.exe ]]; then
+    cp "$BINARY" "$UPDATE_HOME/.local/bin/codebase-memory-mcp.exe"
+    chmod 755 "$UPDATE_HOME/.local/bin/codebase-memory-mcp.exe"
+  else
+    cp "$BINARY" "$UPDATE_HOME/.local/bin/codebase-memory-mcp"
+    chmod 755 "$UPDATE_HOME/.local/bin/codebase-memory-mcp"
+    if [ "$(uname -s)" = "Darwin" ]; then
+      codesign --sign - --force "$UPDATE_HOME/.local/bin/codebase-memory-mcp" 2>/dev/null || true
+    fi
   fi
 
   # Pre-install agent config with a WRONG binary path (simulates stale config)
@@ -1079,7 +1084,7 @@ if [ -n "${SMOKE_DOWNLOAD_URL:-}" ]; then
   HOME="$UPDATE_HOME" "$BINARY" uninstall -y 2>&1 || true
 
   # 14e: Verify binary removed
-  if [ -f "$UPDATE_HOME/.local/bin/codebase-memory-mcp" ]; then
+  if [ -f "$UPDATE_HOME/.local/bin/codebase-memory-mcp" ] || [ -f "$UPDATE_HOME/.local/bin/codebase-memory-mcp.exe" ]; then
     echo "FAIL 14e: binary still exists after uninstall"
     exit 1
   fi

scripts/soak-test.sh

@@ -433,11 +433,12 @@ if [ "${IDLE_INT:-0}" -gt 5 ] 2>/dev/null; then
     PASS=false
 fi
 
-# Check 4: Max query latency
-MAX_LATENCY=$(awk -F, 'NR>1 { if ($3>max) max=$3 } END { print max+0 }' "$LATENCY_CSV")
-echo "Max query latency: ${MAX_LATENCY}ms" | tee -a "$SUMMARY"
+# Check 4: Max query latency (exclude index_repository — indexing is legitimately slow)
+MAX_LATENCY=$(awk -F, 'NR>1 && $2!="index_repository" { if ($3>max) max=$3 } END { print max+0 }' "$LATENCY_CSV")
+MAX_INDEX=$(awk -F, 'NR>1 && $2=="index_repository" { if ($3>max) max=$3 } END { print max+0 }' "$LATENCY_CSV")
+echo "Max query latency: ${MAX_LATENCY}ms (index: ${MAX_INDEX}ms)" | tee -a "$SUMMARY"
 if [ "${MAX_LATENCY:-0}" -gt 10000 ] 2>/dev/null; then
-    echo "FAIL: max latency ${MAX_LATENCY}ms > 10s" | tee -a "$SUMMARY"
+    echo "FAIL: max query latency ${MAX_LATENCY}ms > 10s" | tee -a "$SUMMARY"
     PASS=false
 fi