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diff --git a/test/end-to-end/just-mr/absent-closure.sh b/test/end-to-end/just-mr/absent-closure.sh
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+#!/bin/sh
+# Copyright 2025 Huawei Cloud Computing Technology Co., Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+###
+# Test that users are warned if a non-absent repository is reached from an
+# absent main repository.
+##
+
+set -eu
+
+readonly JUST_MR="${PWD}/bin/mr-tool-under-test"
+readonly FILE_ROOT="${TEST_TMPDIR}/file-repos"
+readonly TEST_ROOT="${TEST_TMPDIR}/test-root"
+readonly LBR="${TEST_TMPDIR}/local-build-root"
+readonly OUT="${TEST_TMPDIR}/out"
+mkdir -p "${OUT}"
+
+# Set up file repos
+mkdir -p "${FILE_ROOT}/test_dir1"
+echo test > "${FILE_ROOT}/test_dir1/test_file"
+mkdir -p "${FILE_ROOT}/test_dir2/inner_dir"
+echo test > "${FILE_ROOT}/test_dir2/inner_dir/test_file"
+mkdir -p "${FILE_ROOT}/test_dir3/inner_dir"
+echo test > "${FILE_ROOT}/test_dir3/inner_dir/test_file"
+
+# Setup sample repository config
+mkdir -p "${TEST_ROOT}"
+cd "${TEST_ROOT}"
+touch ROOT
+cat > repos.json <<EOF
+{ "repositories":
+  { "main":
+    { "repository":
+      { "type": "file"
+      , "path": "."
+      , "pragma": {"absent": true}
+      }
+    , "bindings":
+      { "dep1": "file_repo_not_content_fixed"
+      , "dep2": "file_repo_to_git_explicit"
+      , "dep3": "file_repo_to_git_implicit"
+      }
+    }
+  , "file_repo_not_content_fixed":
+    { "repository":
+      { "type": "file"
+      , "path": "${FILE_ROOT}/test_dir1"
+      }
+    }
+  , "file_repo_to_git_explicit":
+    { "repository":
+      { "type": "file"
+      , "path": "${FILE_ROOT}/test_dir2"
+      , "pragma": {"to_git": true}
+      }
+    }
+  , "file_repo_to_git_implicit":
+    { "repository":
+      { "type": "file"
+      , "path": "${FILE_ROOT}/test_dir3"
+      , "pragma": {"special": "resolve-partially"}
+      }
+    }
+  }
+}
+EOF
+echo "Repository configuration:"
+cat repos.json
+
+echo
+echo Run setup of absent main repository
+echo
+"${JUST_MR}" --norc --local-build-root "${LBR}" -f "${OUT}/log.txt" setup main 2>&1
+
+echo
+echo Check expected warnings
+echo
+
+grep 'WARN.* "main" .*absent.* "main"' "${OUT}/log.txt"
+grep 'WARN.* "file_repo_not_content_fixed" .*absent.* "main"' "${OUT}/log.txt"
+grep 'WARN.* "file_repo_to_git_explicit" .*absent.* "main"' "${OUT}/log.txt" &&
+    echo "should have failed" && exit 1 || :
+grep 'WARN.* "file_repo_to_git_implicit" .*absent.* "main"' "${OUT}/log.txt" &&
+    echo "should have failed" && exit 1 || :
+
+echo
+echo OK