Make RUN_CHECK_WITH_PARALLEL_QUERIES the last thing to run

This takes a long time and rarely fails. It also interferes with `retry make prepare`, the retry is unhelpful since `make prepare` turns into a no-op

src/bootstrap/config.rs

@@ -638,6 +638,7 @@ define_config! {
         dist_stage: Option<u32> = "dist-stage",
         bench_stage: Option<u32> = "bench-stage",
         patch_binaries_for_nix: Option<bool> = "patch-binaries-for-nix",
+        // NOTE: only parsed by bootstrap.py, `--feature build-metrics` enables metrics unconditionally
         metrics: Option<bool> = "metrics",
     }
 }

src/ci/run.sh

@@ -56,6 +56,7 @@ fi
 if ! isCI || isCiBranch auto || isCiBranch beta || isCiBranch try || isCiBranch try-perf; then
     RUST_CONFIGURE_ARGS="$RUST_CONFIGURE_ARGS --set build.print-step-timings --enable-verbose-tests"
     RUST_CONFIGURE_ARGS="$RUST_CONFIGURE_ARGS --set build.metrics"
+    HAS_METRICS=1
 fi
 
 RUST_CONFIGURE_ARGS="$RUST_CONFIGURE_ARGS --enable-sccache"
@@ -157,13 +158,6 @@ trap datecheck EXIT
 # sccache server at the start of the build, but no need to worry if this fails.
 SCCACHE_IDLE_TIMEOUT=10800 sccache --start-server || true
 
-if [ "$RUN_CHECK_WITH_PARALLEL_QUERIES" != "" ]; then
-  $SRC/configure --set rust.parallel-compiler
-  CARGO_INCREMENTAL=0 $PYTHON ../x.py check
-  rm -f config.toml
-  rm -rf build
-fi
-
 $SRC/configure $RUST_CONFIGURE_ARGS
 
 retry make prepare
@@ -193,4 +187,21 @@ else
   do_make "$RUST_CHECK_TARGET"
 fi
 
+if [ "$RUN_CHECK_WITH_PARALLEL_QUERIES" != "" ]; then
+  rm -f config.toml
+  $SRC/configure --set rust.parallel-compiler
+
+  # Save the build metrics before we wipe the directory
+  if [ $HAS_METRICS = 1 ]; then
+    mv build/metrics.json .
+  fi
+  rm -rf build
+  if [ $HAS_METRICS = 1 ]; then
+    mkdir build
+    mv metrics.json build
+  fi
+
+  CARGO_INCREMENTAL=0 $PYTHON ../x.py check
+fi
+
 sccache --show-stats || true