diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9b35208bf32..565c916db5b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -414,7 +414,7 @@ jobs:
             os: windows-latest-xl
           - name: x86_64-msvc-tools
             env:
-              SCRIPT: src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh x.py --stage 2 /tmp/toolstate/toolstates.json windows
+              SCRIPT: src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh x.py /tmp/toolstate/toolstates.json windows
               RUST_CONFIGURE_ARGS: "--build=x86_64-pc-windows-msvc --save-toolstates=/tmp/toolstate/toolstates.json"
             os: windows-latest-xl
           - name: i686-mingw-1
diff --git a/src/bootstrap/flags.rs b/src/bootstrap/flags.rs
index a298b299667..56e4f0467cc 100644
--- a/src/bootstrap/flags.rs
+++ b/src/bootstrap/flags.rs
@@ -425,7 +425,7 @@ Arguments:
     This subcommand accepts a number of paths to tools to build and run. For
     example:
 
-        ./x.py run src/tool/expand-yaml-anchors
+        ./x.py run src/tools/expand-yaml-anchors
 
     At least a tool needs to be called.",
                 );
diff --git a/src/ci/docker/host-x86_64/x86_64-gnu-tools/Dockerfile b/src/ci/docker/host-x86_64/x86_64-gnu-tools/Dockerfile
index e99b3f6ec37..ef17f0507ab 100644
--- a/src/ci/docker/host-x86_64/x86_64-gnu-tools/Dockerfile
+++ b/src/ci/docker/host-x86_64/x86_64-gnu-tools/Dockerfile
@@ -22,4 +22,4 @@ COPY host-x86_64/x86_64-gnu-tools/checktools.sh /tmp/
 ENV RUST_CONFIGURE_ARGS \
   --build=x86_64-unknown-linux-gnu \
   --save-toolstates=/tmp/toolstate/toolstates.json
-ENV SCRIPT /tmp/checktools.sh ../x.py --stage 2
+ENV SCRIPT /tmp/checktools.sh ../x.py
diff --git a/src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh b/src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh
index b4b23a245e0..49a8e5e88a0 100755
--- a/src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh
+++ b/src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh
@@ -7,7 +7,7 @@ X_PY="$1"
 # Try to test all the tools and store the build/test success in the TOOLSTATE_FILE
 
 set +e
-python3 "$X_PY" test --no-fail-fast \
+python3 "$X_PY" test --stage 2 --no-fail-fast \
     src/doc/book \
     src/doc/nomicon \
     src/doc/reference \
@@ -22,5 +22,5 @@ set -e
 
 # debugging: print out the saved toolstates
 cat /tmp/toolstate/toolstates.json
-python3 "$X_PY" test check-tools
-python3 "$X_PY" test src/tools/clippy
+python3 "$X_PY" test --stage 2 check-tools
+python3 "$X_PY" test --stage 2 src/tools/clippy
diff --git a/src/ci/github-actions/ci.yml b/src/ci/github-actions/ci.yml
index b31f00c0322..a7c1987e8b1 100644
--- a/src/ci/github-actions/ci.yml
+++ b/src/ci/github-actions/ci.yml
@@ -481,7 +481,7 @@ jobs:
 
           - name: x86_64-msvc-tools
             env:
-              SCRIPT: src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh x.py --stage 2 /tmp/toolstate/toolstates.json windows
+              SCRIPT: src/ci/docker/host-x86_64/x86_64-gnu-tools/checktools.sh x.py /tmp/toolstate/toolstates.json windows
               RUST_CONFIGURE_ARGS: --build=x86_64-pc-windows-msvc --save-toolstates=/tmp/toolstate/toolstates.json
             <<: *job-windows-xl