diff --git a/.gitignore b/.gitignore
index a1b4284..21eb53f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,5 @@
-/input/
-/output/
+/runtime/
 /dependencies/
-examples
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/.init-container.sh b/.init-container.sh
index 005716d..acff572 100755
--- a/.init-container.sh
+++ b/.init-container.sh
@@ -1,10 +1,7 @@
 #!/bin/bash
 
 
-echo 'export PATH="$EOA_SCRIPTS_DIR:$PATH"' >> ~/.bashrc
-
-ln -s $INPUT_DIR input
-ln -s $OUTPUT_DIR output
+echo 'export PATH="$EOA_SCRIPTS_DIR:$PATH"' > ./.bashrc
 
 # wait, keep container running:
 bash -c 'while :; do :; done & kill -STOP $! && wait $!'
diff --git a/Dockerfile b/Dockerfile
index fef6597..a070e1c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -104,12 +104,5 @@ RUN echo '#!/bin/bash' > $UTILS_BIN_DIR/saxon
 RUN echo 'java -jar $UTILS_BIN_DIR/saxon9he.jar "$@"' >> $UTILS_BIN_DIR/saxon
 RUN chmod ugo+x $UTILS_BIN_DIR/saxon
 
-# create a HOME and reasonable environment settings for the user:
-ENV HOME /home/user
-RUN useradd --create-home user
-WORKDIR ${HOME}
-
-COPY ".init-container.sh" "$HOME/init_container.sh"
-RUN chmod ugo+x "$HOME/init_container.sh"
-
-USER user
+COPY ".init-container.sh" "$UTILS_BIN_DIR/init_container.sh"
+RUN chmod ugo+x "$UTILS_BIN_DIR/init_container.sh"
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 3ebf31f..5d9b0a8 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -6,16 +6,19 @@ services:
     build: .
     image: ${IMAGE_NAME}
     container_name: ${CONTAINER_NAME}
-    command: "/home/user/init_container.sh"
+    command: "/eoa/bin/init_container.sh"
     volumes:
       - ./${SRC_DIR}:${SRC_DIR_IN_CONTAINER}
+      - ./${HOME_DIR}:${HOME_DIR_IN_CONTAINER}
       - ./${INPUT_DIR}:${INPUT_DIR_IN_CONTAINER}
       - ./${OUTPUT_DIR}:${OUTPUT_DIR_IN_CONTAINER}
     environment:
+      - HOME=${HOME_DIR_IN_CONTAINER}
       - INPUT_DIR=${INPUT_DIR_IN_CONTAINER}
       - OUTPUT_DIR=${OUTPUT_DIR_IN_CONTAINER}
       - DEPENDENCIES_DIR=${DEPENDENCIES_DIR_IN_CONTAINER}
       - EOA_SCRIPTS_DIR=${SRC_DIR_IN_CONTAINER}
     ports: []
     user: ${USER}:${GROUP}
+    working_dir: ${HOME_DIR_IN_CONTAINER}
     tty: true
diff --git a/scripts/config/env.conf b/scripts/config/env.conf
index a31514c..b9bcfe0 100644
--- a/scripts/config/env.conf
+++ b/scripts/config/env.conf
@@ -15,15 +15,18 @@ CONTAINER_NAME=eoa_skripts
 SRC_DIR=src
 SRC_DIR_IN_CONTAINER=/eoa/skripts
 
-INPUT_DIR=input
+DEPENDENCIES_DIR=dependencies
+DEPENDENCIES_DIR_IN_CONTAINER=/eoa/dependencies
+
+HOME_DIR=runtime/work_dir
+HOME_DIR_IN_CONTAINER=/home/work_dir
+
+INPUT_DIR=runtime/input
 INPUT_DIR_IN_CONTAINER=/eoa/input
 
-OUTPUT_DIR=output
+OUTPUT_DIR=runtime/output
 OUTPUT_DIR_IN_CONTAINER=/eoa/output
 
-DEPENDENCIES_DIR=dependencies
-DEPENDENCIES_DIR_IN_CONTAINER=/eoa/dependencies
-
 ###################################################
 # user and group:
 # USER=$(id -u)
diff --git a/scripts/init.py b/scripts/init.py
index 6d15b1f..d20d282 100755
--- a/scripts/init.py
+++ b/scripts/init.py
@@ -37,12 +37,27 @@ def create_dirs( config ):
     create_dir(
         BASE_DIR / config['DEPENDENCIES_DIR']
     )
+    create_dir(
+        BASE_DIR / config['HOME_DIR']
+    )
     create_dir(
         BASE_DIR / config['INPUT_DIR']
     )
     create_dir(
         BASE_DIR / config['OUTPUT_DIR']
     )
+    in_link = Path(BASE_DIR / config['HOME_DIR'] / 'input' )
+    if not(in_link.is_symlink()) and not(in_link.exists()):
+        in_link . symlink_to(
+            config['INPUT_DIR_IN_CONTAINER'],
+            target_is_directory = True,
+        )
+    out_link = Path(BASE_DIR / config['HOME_DIR'] / 'output' )
+    if not(out_link.is_symlink()) and not(out_link.exists()):
+        out_link . symlink_to(
+            config['OUTPUT_DIR_IN_CONTAINER'],
+            target_is_directory = True,
+        )
 
 def install_git_dep(
     repo_name,
@@ -126,7 +141,7 @@ def install_git_dep(
             env = config,
         )
 
-    # copy example publication to $INPUT_DIR
+    # copy example publication to $INPUT_DIR:
     copy_dir(
         BASE_DIR / config['DEPENDENCIES_DIR'] / 'eoa-publication-model/examples',
         BASE_DIR / config['INPUT_DIR'] / 'example'