diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index caab87d0b..dedb827a0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -292,7 +292,7 @@ jobs:
 
     defaults:
       run:
-        working-directory: ./server/app
+        working-directory: ./server
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ env.X_PYTHON_MIN_VERSION }}
@@ -302,26 +302,26 @@ jobs:
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install ../../sdk
+        python -m pip install ../sdk
         python -m pip install .[dev]
     - name: Check typing with MyPy
       run: |
-        python -m mypy .
+        python -m mypy app test
     - name: Check code style with PyCodestyle
       run: |
-        python -m pycodestyle --count --max-line-length 120 .
+        python -m pycodestyle --count --max-line-length 120 app test
 
-  server-package:
+  server-repository-docker:
     # This job checks if we can build our server package
     runs-on: ubuntu-latest
     defaults:
       run:
-        working-directory: ./server
+        working-directory: ./server/docker/repository
     steps:
       - uses: actions/checkout@v4
       - name: Build the Docker image
         run: |
-          docker build -t basyx-python-server -f Dockerfile ..
+          docker build -t basyx-python-server -f Dockerfile ../../..
       - name: Run container
         run: |
            docker run -d --name basyx-python-server basyx-python-server
diff --git a/server/README.md b/server/README.md
index d368d4ae5..0d5203f9b 100644
--- a/server/README.md
+++ b/server/README.md
@@ -19,7 +19,7 @@ The container image can be built via:
 $ docker build -t basyx-python-server -f Dockerfile ..
 ```
 
-Note that when cloning this repository on Windows, Git may convert the line separators to CRLF. This breaks [`entrypoint.sh`](entrypoint.sh) and [`stop-supervisor.sh`](stop-supervisor.sh). Ensure both files use LF line separators (`\n`) before building. 
+Note that when cloning this repository on Windows, Git may convert the line separators to CRLF. This breaks [`entrypoint.sh`](docker/repository/entrypoint.sh) and [`stop-supervisor.sh`](docker/common/stop-supervisor.sh). Ensure both files use LF line separators (`\n`) before building. 
 
 ## Running
 
@@ -60,51 +60,13 @@ This implies the following start-up behaviour:
   - Any AAS/Submodel *already present* is skipped, unless `STORAGE_OVERWRITE = True`, in which case it is replaced.
 - Supplementary files (e.g., `File` SubmodelElements) are never persisted by the LocalFileBackend.
 
-### Running Examples
-
-Putting it all together, the container can be started via the following command:
-```
-$ docker run -p 8080:80 -v ./input:/input -v ./storage:/storage basyx-python-server
-```
-
-Since Windows uses backslashes instead of forward slashes in paths, you'll have to adjust the path to the storage directory there:
-```
-> docker run -p 8080:80 -v .\input:/input -v .\storage:/storage basyx-python-server
-```
-
-By default, the server will use the standard settings described [above](#options). Those settings can be adapted in the following way:
-```
-$ docker run -p 8080:80 -v ./input:/input2 -v ./storage:/storage2 -e API_BASE_PATH=/api/v3.1/ -e INPUT=/input2 -e STORAGE=/storage2 -e STORAGE_PERSISTENCY=True -e STORAGE_OVERWRITE=True basyx-python-server
-```
-
 ## Building and Running the Image with Docker Compose
 
-The container image can also be built and run via:
-```
-$ docker compose up
-```
-
-An exemplary [`compose.yml`](compose.yml) file for the server is given [here](compose.yml):
-```yaml
-name: basyx-python-server
-services:
-  app:
-    build:
-      context: ..
-      dockerfile: server/Dockerfile
-    ports:
-    - "8080:80"
-    volumes:
-      - ./input:/input
-      - ./storage:/storage
-    environment:
-      STORAGE_PERSISTENCY: True
-```
+Example configurations can be found in the `./example_configurations` directory.
 
-Input files are read from `./input` and stored persistently under `./storage` on your host system. The server can be accessed at http://localhost:8080/api/v3.0/ from your host system. 
-To get a different setup, the [`compose.yml`](compose.yml) file can be adapted using the options described [above](#options), similar to the third [running example](#running-examples).
+Currently, we offer: 
 
-Note that the `Dockerfile` has to be specified explicitly via `dockerfile: server/Dockerfile`, as the build context must be set to the parent directory of `/server` to allow access to the local `/sdk`.
+- [repository_standalone](example_configurations/repository_standalone/README.md): Standalone repository server
 
 ## Running without Docker (Debugging Only)
 
diff --git a/server/app/__init__.py b/server/app/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/server/app/interfaces/base.py b/server/app/interfaces/base.py
index 360ba8514..8234eddc2 100644
--- a/server/app/interfaces/base.py
+++ b/server/app/interfaces/base.py
@@ -25,7 +25,7 @@
 from basyx.aas.adapter.json import StrictStrippedAASFromJsonDecoder, StrictAASFromJsonDecoder, AASToJsonEncoder
 from basyx.aas.adapter.xml import xml_serialization, XMLConstructables, read_aas_xml_element
 from basyx.aas.model import AbstractObjectStore
-from util.converters import base64url_decode
+from app.util.converters import base64url_decode
 
 
 T = TypeVar("T")
diff --git a/server/app/interfaces/repository.py b/server/app/interfaces/repository.py
index 18976c81b..c1ee513e5 100644
--- a/server/app/interfaces/repository.py
+++ b/server/app/interfaces/repository.py
@@ -22,7 +22,7 @@
 
 from basyx.aas import model
 from basyx.aas.adapter import aasx
-from util.converters import IdentifierToBase64URLConverter, IdShortPathConverter, base64url_decode
+from app.util.converters import IdentifierToBase64URLConverter, IdShortPathConverter, base64url_decode
 from .base import ObjectStoreWSGIApp, APIResponse, is_stripped_request, HTTPApiDecoder, T
 
 
diff --git a/server/app/services/__init__.py b/server/app/services/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/server/app/main.py b/server/app/services/run_repository.py
similarity index 99%
rename from server/app/main.py
rename to server/app/services/run_repository.py
index 3b37edab2..478e4d215 100644
--- a/server/app/main.py
+++ b/server/app/services/run_repository.py
@@ -14,7 +14,7 @@
 from basyx.aas.adapter.aasx import DictSupplementaryFileContainer
 from basyx.aas.backend.local_file import LocalFileIdentifiableStore
 from basyx.aas.model.provider import DictIdentifiableStore
-from interfaces.repository import WSGIApp
+from app.interfaces.repository import WSGIApp
 from typing import Tuple, Union
 
 
diff --git a/server/stop-supervisor.sh b/server/docker/common/stop-supervisor.sh
similarity index 100%
rename from server/stop-supervisor.sh
rename to server/docker/common/stop-supervisor.sh
diff --git a/server/supervisord.ini b/server/docker/common/supervisord.ini
similarity index 100%
rename from server/supervisord.ini
rename to server/docker/common/supervisord.ini
diff --git a/server/Dockerfile b/server/docker/repository/Dockerfile
similarity index 72%
rename from server/Dockerfile
rename to server/docker/repository/Dockerfile
index 7ad70bc66..eed1c1abe 100644
--- a/server/Dockerfile
+++ b/server/docker/repository/Dockerfile
@@ -15,10 +15,14 @@ RUN apk update && \
     pip install uwsgi && \
     apk del git bash
 
-
-COPY server/uwsgi.ini /etc/uwsgi/
-COPY server/supervisord.ini /etc/supervisor/conf.d/supervisord.ini
-COPY server/stop-supervisor.sh /etc/supervisor/stop-supervisor.sh
+# Copy only the files we need to run the container
+# The argumentation for this is to keep the containers as slim as possible.
+COPY ./sdk /sdk
+COPY ./server/app /server/app
+COPY ./server/pyproject.toml /server/pyproject.toml
+COPY ./server/docker/repository/uwsgi.ini /etc/uwsgi/
+COPY ./server/docker/common/supervisord.ini /etc/supervisor/conf.d/supervisord.ini
+COPY ./server/docker/common/stop-supervisor.sh /etc/supervisor/stop-supervisor.sh
 RUN chmod +x /etc/supervisor/stop-supervisor.sh
 
 # Makes it possible to use a different configuration
@@ -41,17 +45,15 @@ ENV STORAGE_OVERWRITE=False
 VOLUME ["/input", "/storage"]
 
 # Copy the entrypoint that will generate Nginx additional configs
-COPY server/entrypoint.sh /entrypoint.sh
+COPY server/docker/repository/entrypoint.sh /entrypoint.sh
 RUN chmod +x /entrypoint.sh
 
 ENTRYPOINT ["/entrypoint.sh"]
 
 ENV SETUPTOOLS_SCM_PRETEND_VERSION=1.0.0
 
-COPY ./sdk /sdk
-COPY ./server/app /app
-WORKDIR /app
-RUN pip install ../sdk
-RUN pip install .
+WORKDIR /server/app
+RUN pip install ../../sdk
+RUN pip install ..
 
 CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.ini"]
diff --git a/server/entrypoint.sh b/server/docker/repository/entrypoint.sh
similarity index 100%
rename from server/entrypoint.sh
rename to server/docker/repository/entrypoint.sh
diff --git a/server/uwsgi.ini b/server/docker/repository/uwsgi.ini
similarity index 79%
rename from server/uwsgi.ini
rename to server/docker/repository/uwsgi.ini
index 9c54ae1cc..ac4294aca 100644
--- a/server/uwsgi.ini
+++ b/server/docker/repository/uwsgi.ini
@@ -1,5 +1,5 @@
 [uwsgi]
-wsgi-file = /app/main.py
+wsgi-file = /server/app/services/run_repository.py
 socket = /tmp/uwsgi.sock
 chown-socket = nginx:nginx
 chmod-socket = 664
diff --git a/server/example_configurations/repository_standalone/README.md b/server/example_configurations/repository_standalone/README.md
new file mode 100644
index 000000000..ce84c5f67
--- /dev/null
+++ b/server/example_configurations/repository_standalone/README.md
@@ -0,0 +1,15 @@
+# Repository Standalone
+
+This example Docker compose configuration starts a repository server. 
+
+The container image can also be built and run via:
+```
+$ docker compose up
+```
+
+Input files are read from `./input` and stored persistently under `./storage` on your host system. 
+The server can be accessed at http://localhost:8080/api/v3.0/ from your host system. 
+To get a different setup, the `compose.yaml` file can be adapted using the options described in the main server [README.md](../../README.md#options).
+
+Note that the `Dockerfile` has to be specified explicitly via `dockerfile: server/docker/repository/Dockerfile`, as the build context must be set to the repository root to allow access to the local `/sdk`.
+
diff --git a/server/compose.yml b/server/example_configurations/repository_standalone/compose.yaml
similarity index 71%
rename from server/compose.yml
rename to server/example_configurations/repository_standalone/compose.yaml
index f7e014c37..10e8b17f1 100644
--- a/server/compose.yml
+++ b/server/example_configurations/repository_standalone/compose.yaml
@@ -2,8 +2,8 @@ name: basyx-python-server
 services:
   app:
     build:
-      context: ..
-      dockerfile: server/Dockerfile
+      context: ../../..
+      dockerfile: server/docker/repository/Dockerfile
     ports:
     - "8080:80"
     volumes:
diff --git a/server/app/pyproject.toml b/server/pyproject.toml
similarity index 90%
rename from server/app/pyproject.toml
rename to server/pyproject.toml
index 030be7397..8c40deff9 100644
--- a/server/app/pyproject.toml
+++ b/server/pyproject.toml
@@ -16,8 +16,8 @@ build-backend = "setuptools.build_meta"
 # from app.version import version
 # print(f"Project version: {version}")
 # ```
-root = "../.."  # Defines the path to the root of the repository
-version_file = "version.py"
+root = ".."  # Defines the path to the root of the repository
+version_file = "app/version.py"
 
 [project]
 name = "basyx-python-server"
@@ -55,7 +55,7 @@ dev = [
 "Homepage" = "https://github.com/eclipse-basyx/basyx-python-sdk"
 
 [tool.setuptools]
-packages = { find = { exclude = ["test*"] } }
+packages = { find = { include = ["app*"], exclude = ["test*"] } }
 
 [tool.setuptools.package-data]
 app = ["py.typed"]
diff --git a/server/test/interfaces/test_repository.py b/server/test/interfaces/test_repository.py
index 0c7f4c1a8..5cf421a51 100644
--- a/server/test/interfaces/test_repository.py
+++ b/server/test/interfaces/test_repository.py
@@ -34,7 +34,7 @@
 
 from basyx.aas import model
 from basyx.aas.adapter.aasx import DictSupplementaryFileContainer
-from server.app.interfaces.repository import WSGIApp
+from app.interfaces.repository import WSGIApp
 from basyx.aas.examples.data.example_aas import create_full_example
 
 from typing import Set