diff --git a/.gitignore b/.gitignore
index b0decb2aa4b117cf8cac3569140c693fe78773ea..14140a23bf24c01df069e7251eeae28ff0834364 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,13 +1,10 @@
-/nbproject
-/Debug
-/Release
-/RelWithDebInfo
-/Testing
+# build/output directories
+/builddir
 /Documentation/html/
 /Documentation/output_snippets/
-/CMakeLists.txt.user
-/Build
-/coverage_report
+
+# Netbeans project stuff
+/nbproject
 
 # Eclipse project stuff
 /.settings
@@ -25,3 +22,10 @@
 
 # GDB
 .gdb_history
+
+# old/deprecated directories (can be removed later, they are not used anymore)
+/Debug
+/Release
+/RelWithDebInfo
+/Testing
+/Build
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ad6baa05ffa7267bd11aad0aead25861aa2bc520..85b56388bd14774a3d6942407e92703b6ddd307a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -36,13 +36,6 @@ stages:
         WITH_OPENMP: "yes"
         WITH_MPI: "yes"
 
-.cuda_openmp_mpi:
-    extends: .openmp_mpi
-    # tags are overridden, not merged...
-    tags:
-        - docker
-        - nvidia
-
 # base for Clang builds
 .clang:
     stage: build:clang
@@ -71,12 +64,13 @@ stages:
         # running as root does not matter inside Docker containers
         - export OMPI_ALLOW_RUN_AS_ROOT=1
         - export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-        - mkdir -p "./builddir/$CI_JOB_NAME"
-        - pushd "./builddir/$CI_JOB_NAME"
-        - cmake ../..
-                -G Ninja
+        # fall back to arch 7.0 when the builder has no GPU to avoid building for all GPU architectures
+        - if ! nvidia-smi --list-gpus > /dev/null; then
+                WITH_CUDA_ARCH=7.0;
+          fi
+        - cmake -B "./builddir/$CI_JOB_NAME" -S . -G Ninja
                 -DCMAKE_BUILD_TYPE=${BUILD_TYPE}
-                -DCMAKE_INSTALL_PREFIX="$(pwd)/${BUILD_TYPE}_install_prefix"
+                -DCMAKE_INSTALL_PREFIX="$(pwd)/install_prefix/$CI_JOB_NAME"
                 -DWITH_OPENMP=${WITH_OPENMP}
                 -DWITH_MPI=${WITH_MPI}
                 -DWITH_CUDA=${WITH_CUDA}
@@ -91,11 +85,10 @@ stages:
                 -DBUILD_PYTHON=${BUILD_PYTHON}
                 -DWITH_CI_FLAGS=yes
         # "install" implies the "all" target
-        - ninja ${NINJAFLAGS} install
+        - ninja -C "./builddir/$CI_JOB_NAME" ${NINJAFLAGS} install
         - if [[ ${BUILD_TESTS} == "yes" ]] || [[ ${BUILD_MATRIX_TESTS} == "yes" ]]; then
-                ninja test;
+                ninja -C "./builddir/$CI_JOB_NAME" test;
           fi
-        - popd
     variables:
         <<: *default_cmake_flags
         BUILD_TYPE: Debug
@@ -180,9 +173,6 @@ cuda_matrix_tests_Release:
 cuda_nontests_Debug:
     extends: .build_template
     stage: build:cuda
-    tags:
-        - docker
-        - nvidia
     variables:
         <<: *default_cmake_flags
         WITH_CUDA: "yes"
@@ -195,9 +185,6 @@ cuda_nontests_Debug:
 cuda_nontests_Release:
     extends: .build_template
     stage: build:cuda
-    tags:
-        - docker
-        - nvidia
     variables:
         <<: *default_cmake_flags
         WITH_CUDA: "yes"
@@ -211,32 +198,32 @@ cuda_nontests_Release:
 cuda_mpi_tests_Debug:
     extends:
         - cuda_tests_Debug
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 cuda_mpi_tests_Release:
     extends:
         - cuda_tests_Release
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 cuda_mpi_matrix_tests_Debug:
     extends:
         - cuda_matrix_tests_Debug
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 cuda_mpi_matrix_tests_Release:
     extends:
         - cuda_matrix_tests_Release
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 cuda_mpi_nontests_Debug:
     extends:
         - cuda_nontests_Debug
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 cuda_mpi_nontests_Release:
     extends:
         - cuda_nontests_Release
-        - .cuda_openmp_mpi
+        - .openmp_mpi
 
 
 
diff --git a/Documentation/fetch-outputs b/Documentation/fetch-outputs
deleted file mode 100755
index bb1a669b54686dbee4d0d9b8b17c1bc66d5b8383..0000000000000000000000000000000000000000
--- a/Documentation/fetch-outputs
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-
-OUTPUTS_PATH=../Release/src/Examples
-
-DOC_ROOT_DIR=`pwd`
-
-echo $DOC_ROOT_DIR
-
-mkdir Outputs
-
-find $OUTPUTS_PATH -name "*.out" -exec echo '{}' Outputs/'{}' \;
-
diff --git a/build b/build
index aa764ae81a5b1d413e1b2320ea53f42025c02988..1850c17583c21a41a102533f698f2cec6db715c6 100755
--- a/build
+++ b/build
@@ -145,10 +145,6 @@ if [[ ! "Release Debug RelWithDebInfo" =~ "$BUILD" ]]; then
     echo "Unknown build type: $BUILD. The available build types are: Release, Debug, RelWithDebInfo." >&2
     exit 1
 fi
-if [[ ! -d "$BUILD" ]]; then
-    mkdir "$BUILD"
-fi
-pushd "$BUILD" >/dev/null
 
 # handle targets
 for target in "$@"; do
@@ -209,9 +205,13 @@ else
    check_file="Makefile"
 fi
 
+# remove old build directories that were used before the unified top-level "builddir"
+# (TODO: this code be removed later)
+rm -rf ./Release ./Debug ./RelWithDebInfo ./Testing ./Build
+
+BUILD_DIR="builddir/$BUILD"
 cmake_command=(
-   ${CMAKE} ${ROOT_DIR}
-         -G "${generator}"
+   ${CMAKE} -B "$BUILD_DIR" -S "$ROOT_DIR" -G "$generator"
          -DCMAKE_BUILD_TYPE=${BUILD}
          -DCMAKE_INSTALL_PREFIX=${PREFIX}
          -DDCMTK_DIR=${DCMTK_DIR}
@@ -238,14 +238,14 @@ cmake_command=(
 # The build system (e.g. make) will call it automatically if necessary (e.g.
 # when some CMakeLists.txt changes).
 if [[ -f ".cmake_command" ]]; then
-   last_cmake_command=$(cat ".cmake_command" 2>/dev/null)
+   last_cmake_command=$(cat "$BUILD_DIR/.cmake_command" 2>/dev/null)
 else
    last_cmake_command=""
 fi
 if [[ ! -f "$check_file" ]] || [[ "$last_cmake_command" != "${cmake_command[@]}" ]]; then
    echo "Configuring ${BUILD} TNL ..."
    "${cmake_command[@]}"
-   echo -n "${cmake_command[@]}" > ".cmake_command"
+   echo -n "${cmake_command[@]}" > "$BUILD_DIR/.cmake_command"
 fi
 
 if [[ ${CMAKE_ONLY} == "yes" ]]; then
@@ -294,7 +294,7 @@ if [[ "$make" != "make" ]] && [[ "$VERBOSE" ]]; then
    VERBOSE="-v"
 fi
 
-if ! $make ${VERBOSE} $make_target; then
+if ! $make -C "$BUILD_DIR" ${VERBOSE} $make_target; then
    exit 1
 fi
 
@@ -304,6 +304,6 @@ fi
 
 if [[ ${BUILD_TESTS} == "yes" ]] || [[ ${BUILD_MATRIX_TESTS} == "yes" ]]; then
    if [[ ${RUN_TESTS} == "yes" ]]; then
-      OMP_NUM_THREADS=${TESTS_JOBS} CTEST_PARALLEL_LEVEL=${TESTS_JOBS} CTEST_OUTPUT_ON_FAILURE=1 $make test
+      OMP_NUM_THREADS=${TESTS_JOBS} CTEST_PARALLEL_LEVEL=${TESTS_JOBS} CTEST_OUTPUT_ON_FAILURE=1 $make -C "$BUILD_DIR" test
    fi
 fi
diff --git a/scripts/make_coverage_report b/scripts/make_coverage_report
index e0c9f1820b900decc218fbdfc555b776e7452fda..645158a302012f92c9c31c7bf9d06b53fca0c62b 100755
--- a/scripts/make_coverage_report
+++ b/scripts/make_coverage_report
@@ -80,4 +80,4 @@ tests=(
 )
 
 # run the programs and create coverage reports
-./scripts/code_coverage/coverage.py -b Debug -o coverage_report/ --ignore-filename-regex="^\/tmp\/tmpxft_.*" "${tests[@]}"
+./scripts/code_coverage/coverage.py -b builddir/Debug -o builddir/coverage_report/ --ignore-filename-regex="^\/tmp\/tmpxft_.*" "${tests[@]}"