diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 4c80a2649a..1d0f3ed470 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -218,6 +218,46 @@ fi
 # Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
 export EESSI_OVERRIDE_GPU_CHECK=1
 
+# before we actually install software, we need to remove software that is requested
+# to be rebuilt (need to do this here because installations of software are read-only;
+# also, it should be done in the same container run or fuse-overlayfs might get confused)
+changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
+if [ -z ${changed_easystacks_rebuilds} ]; then
+    echo "No software needs to be removed."
+else
+    for easystack_file in ${changed_easystacks_rebuilds}; do
+        # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+        # load EasyBuild module (will be installed if it's not available yet)
+        source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
+
+        if [ -f ${easystack_file} ]; then
+            echo_green "Software rebuild(s) requested in ${easystack_file}, so"
+            echo_green "  determining which existing installation have to be removed (assuming contents"
+            echo_green "  have been made writable/deletable)..."
+            # we need to remove existing installation directories first,
+            # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+            #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+            # rebuild_apps=$(eb --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+            rebuild_apps=$(eb --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+            for app in ${rebuild_apps}; do
+                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                ls -lisaR ${app_dir}
+                ls -lisaR ${app_module}
+                echo_yellow "Removing ${app_dir} and ${app_module}..."
+                rm -rdfv ${app_dir}
+                rm -rdfv ${app_module}
+                ls -lisaR ${app_dir}
+                ls -lisaR ${app_module}
+            done
+        else
+            fatal_error "Easystack file ${easystack_file} not found!"
+        fi
+    done
+fi
+
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then
diff --git a/bot/build.sh b/bot/build.sh
index a12d3669fc..2b08a8599c 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -233,31 +233,33 @@ else
 
     ls -lR ${STORAGE}/lower_dirs
 
-    # prepare directory to store tarball of tmp for removal and build steps
-    TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step
-    mkdir -p ${TARBALL_TMP_REMOVAL_STEP_DIR}
-
-    # prepare arguments to eessi_container.sh specific to remove step
-    declare -a REMOVAL_STEP_ARGS=()
-    REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_REMOVAL_STEP_DIR}")
-    REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
-    if [[ ! -z ${LOWER_DIRS} ]]; then
-        REMOVAL_STEP_ARGS+=("--lower-dirs" "${LOWER_DIRS}")
-    fi
-
-    # create tmp file for output of removal step
-    removal_outerr=$(mktemp remove.outerr.XXXX)
-
-    echo "Executing command to remove software:"
-    echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
-    echo "                     -- ./EESSI-remove-software.sh \"${REMOVAL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
-    ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
-                         -- ./EESSI-remove-software.sh "${REMOVAL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
-
-    # make sure that the build step resumes from the same temporary directory
-    # this is important, as otherwise the removed software will still be there
-    REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2)
-    BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
+#    # prepare directory to store tarball of tmp for removal and build steps
+#    TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step
+#    mkdir -p ${TARBALL_TMP_REMOVAL_STEP_DIR}
+#
+####
+#    # prepare arguments to eessi_container.sh specific to remove step
+#    declare -a REMOVAL_STEP_ARGS=()
+#    REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_REMOVAL_STEP_DIR}")
+#    REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
+#    if [[ ! -z ${LOWER_DIRS} ]]; then
+#        REMOVAL_STEP_ARGS+=("--lower-dirs" "${LOWER_DIRS}")
+#    fi
+#
+#    # create tmp file for output of removal step
+#    removal_outerr=$(mktemp remove.outerr.XXXX)
+#
+#    echo "Executing command to remove software:"
+#    echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
+#    echo "                     -- ./EESSI-remove-software.sh \"${REMOVAL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
+#    ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
+#                         -- ./EESSI-remove-software.sh "${REMOVAL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
+#
+#    # make sure that the build step resumes from the same temporary directory
+#    # this is important, as otherwise the removed software will still be there
+#    REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2)
+#    BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
+####
 fi
 
 # prepare directory to store tarball of tmp for build step
@@ -273,20 +275,21 @@ if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
 if [[ ! -z ${LOWER_DIRS} ]]; then
-    # make copy of LOWER_DIRS but only retain directories
-    lower_parent_dir=$(dirname ${LOWER_DIRS})
-    the_lower_dir=$(basename ${LOWER_DIRS})
-    LOWER_DIRS_ONLY="${lower_parent_dir}/${the_lower_dir}_2"
-    mkdir -p ${LOWER_DIRS_ONLY}
-    echo "contents of LOWER_DIRS_ONLY (after mkdir -p)"
-    ls -lisaR ${LOWER_DIRS_ONLY}
-    cp -a ${LOWER_DIRS}/. ${LOWER_DIRS_ONLY}
-    echo "contents of LOWER_DIRS_ONLY (after cp -a)"
-    ls -lisaR ${LOWER_DIRS_ONLY}
-    find ${LOWER_DIRS_ONLY} -type f -exec rm {} \;
-    echo "contents of LOWER_DIRS_ONLY (find ... rm)"
-    ls -lisaR ${LOWER_DIRS_ONLY}
-    BUILD_STEP_ARGS+=("--lower-dirs" "${LOWER_DIRS_ONLY}")
+#    # make copy of LOWER_DIRS but only retain directories
+#    lower_parent_dir=$(dirname ${LOWER_DIRS})
+#    the_lower_dir=$(basename ${LOWER_DIRS})
+#    LOWER_DIRS_ONLY="${lower_parent_dir}/${the_lower_dir}_2"
+#    mkdir -p ${LOWER_DIRS_ONLY}
+#    echo "contents of LOWER_DIRS_ONLY (after mkdir -p)"
+#    ls -lisaR ${LOWER_DIRS_ONLY}
+#    cp -a ${LOWER_DIRS}/. ${LOWER_DIRS_ONLY}
+#    echo "contents of LOWER_DIRS_ONLY (after cp -a)"
+#    ls -lisaR ${LOWER_DIRS_ONLY}
+#    find ${LOWER_DIRS_ONLY} -type f -exec rm {} \;
+#    echo "contents of LOWER_DIRS_ONLY (find ... rm)"
+#    ls -lisaR ${LOWER_DIRS_ONLY}
+#    BUILD_STEP_ARGS+=("--lower-dirs" "${LOWER_DIRS_ONLY}")
+    BUILD_STEP_ARGS+=("--lower-dirs" "${LOWER_DIRS}")
 fi
 
 # create tmp file for output of build step