From 08778d7aacaeaed5dc4fa698b20fca6cda96f087 Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Fri, 2 Oct 2026 16:44:38 +0200
Subject: [PATCH 1/7] Move docker compose assets into docker directory

---
 .github/workflows/ci_job.yml                  |  4 ++
 dev.sh                                        |  8 ++--
 .../docker-compose.dev.yml                    | 44 +++++++++----------
 .../docker-compose.yml                        | 20 ++++-----
 gen_compose.py => docker/gen_compose.py       |  9 ++--
 prod.sh                                       |  8 ++--
 tests/unit_tests/test_gen_compose.py          |  4 +-
 tests/unit_tests/test_prod_sh.py              | 37 ++++++++++++----
 8 files changed, 79 insertions(+), 55 deletions(-)
 rename docker-compose.dev.yml => docker/docker-compose.dev.yml (93%)
 rename docker-compose.yml => docker/docker-compose.yml (91%)
 rename gen_compose.py => docker/gen_compose.py (97%)

diff --git a/.github/workflows/ci_job.yml b/.github/workflows/ci_job.yml
index 7ccd902d..a6c34bdb 100644
--- a/.github/workflows/ci_job.yml
+++ b/.github/workflows/ci_job.yml
@@ -33,6 +33,8 @@ jobs:
   dev-tests:
     name: Full test suite on dev stack (Python 3.13)
     runs-on: ubuntu-latest
+    env:
+      COMPOSE_FILE: docker/docker-compose.dev.yml
 
     steps:
       - name: Checkout
@@ -85,6 +87,8 @@ jobs:
   prod-smoke:
     name: Production smoke test
     runs-on: ubuntu-latest
+    env:
+      COMPOSE_FILE: docker/docker-compose.yml
 
     steps:
       - name: Checkout
diff --git a/dev.sh b/dev.sh
index 886ef18f..09aecfa8 100755
--- a/dev.sh
+++ b/dev.sh
@@ -23,7 +23,7 @@ Custom options:
   --debug, --DEBUG  Enable debug mode (CLIMATECLAW_DEBUG=1)
   --debug=VALUE     Set debug explicitly, e.g. --debug=0 or --debug=1
   --no-debug        Disable debug mode
-  --scale           Generate and use docker-compose.dev.scaled.yml
+  --scale           Generate and use docker/docker-compose.dev.scaled.yml
   --build           Build images before starting
 
 Examples:
@@ -43,7 +43,7 @@ EOF
 export CLIMATECLAW_DEV=1
 
 CLIMATECLAW_DEBUG="${CLIMATECLAW_DEBUG:-0}"
-COMPOSE_FILE="docker-compose.dev.yml"
+COMPOSE_FILE="docker/docker-compose.dev.yml"
 BUILD_COMPOSE_FILE="${COMPOSE_FILE}"
 DO_BUILD=0
 COMPOSE_ARGS=()
@@ -69,8 +69,8 @@ for arg in "$@"; do
       ;;
     # Launch with scaling and proxy
     --scale)
-      ./gen_compose.py ${COMPOSE_FILE}
-      COMPOSE_FILE="docker-compose.dev.scaled.yml"
+      ./docker/gen_compose.py "${COMPOSE_FILE}"
+      COMPOSE_FILE="docker/docker-compose.dev.scaled.yml"
       ;;
     # Build images once from the unscaled compose file.
     --build)
diff --git a/docker-compose.dev.yml b/docker/docker-compose.dev.yml
similarity index 93%
rename from docker-compose.dev.yml
rename to docker/docker-compose.dev.yml
index 062dd5ef..e583015e 100644
--- a/docker-compose.dev.yml
+++ b/docker/docker-compose.dev.yml
@@ -1,7 +1,7 @@
 services:
   climateclaw-base:
     build:
-      context: .
+      context: ..
       dockerfile: docker/Dockerfile.base
     image: ghcr.io/freva-org/climateclaw-base:latest
     profiles:
@@ -10,9 +10,9 @@ services:
   climateclaw:
     image: climateclaw-${CLIMATECLAW_INSTANCE_NAME:?Instance name must be set in the .env file to differentiate between instances}
     build:
-      context: .
+      context: ..
       dockerfile: docker/climateclaw/Dockerfile
-    env_file: .env
+    env_file: ../.env
     environment:
       CLIMATECLAW_DEV: ${CLIMATECLAW_DEV}
       CLIMATECLAW_DEBUG: ${CLIMATECLAW_DEBUG:-0}
@@ -22,8 +22,8 @@ services:
       - "8600:${CLIMATECLAW_BACKEND_PORT:-8502}" # localhost:8600/docs give FastAPI docs
       - "${CLIMATECLAW_DEBUG_PORT:-5678}:${CLIMATECLAW_DEBUG_PORT:-5678}" # Port for debugpy
     volumes:
-      - ./cache/:/app/cache
-      - ./logs/:/app/logs
+      - ../cache/:/app/cache
+      - ../logs/:/app/logs
     networks:
       - climateclaw
     healthcheck:
@@ -41,9 +41,9 @@ services:
   rag-server:
     image: rag-server-${CLIMATECLAW_INSTANCE_NAME}
     build:
-      context: .
+      context: ..
       dockerfile: docker/rag-server/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: rag-server-${CLIMATECLAW_INSTANCE_NAME}
     environment:
       CLIMATECLAW_DEV: ${CLIMATECLAW_DEV}
@@ -51,17 +51,17 @@ services:
       CLIMATECLAW_MCP_HOST: 0.0.0.0
       CLIMATECLAW_MCP_PORT: ${CLIMATECLAW_RAG_PORT:-8050}
     volumes:
-      - ./resources:/app/resources:ro
-      - ./logs/:/app/logs
+      - ../resources:/app/resources:ro
+      - ../logs/:/app/logs
     networks:
       - climateclaw
 
   code-server:
     image: code-server-${CLIMATECLAW_INSTANCE_NAME}
     build:
-      context: .
+      context: ..
       dockerfile: docker/code-server/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: code-server-${CLIMATECLAW_INSTANCE_NAME}
     environment:
       CLIMATECLAW_DEV: ${CLIMATECLAW_DEV}
@@ -72,8 +72,8 @@ services:
       - 8051:8051
     cpus: 4
     volumes:
-      - ./cache/:/app/cache
-      - ./logs/:/app/logs
+      - ../cache/:/app/cache
+      - ../logs/:/app/logs
     networks:
       - climateclaw
     healthcheck:
@@ -86,9 +86,9 @@ services:
   web-search-server:
     image: web-search-server-${CLIMATECLAW_INSTANCE_NAME}
     build:
-      context: .
+      context: ..
       dockerfile: docker/web-search-server/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: web-search-server-${CLIMATECLAW_INSTANCE_NAME}
     environment:
       CLIMATECLAW_DEV: ${CLIMATECLAW_DEV}
@@ -100,7 +100,7 @@ services:
     networks:
       - climateclaw
     volumes:
-      - ./logs/:/app/logs
+      - ../logs/:/app/logs
     healthcheck:
       test: ["CMD-SHELL", "python -c \"import urllib.request; urllib.request.urlopen('http://127.0.0.1:8052/healthz')\""]
       interval: 30s
@@ -112,8 +112,8 @@ services:
     image: ghcr.io/berriai/litellm:main-latest
     hostname: litellm-${CLIMATECLAW_INSTANCE_NAME}
     volumes:
-      - ./litellm_config.yaml:/app/config.yaml # Mount the local litellm_config.yaml file to the container
-      - ./logs/:/app/logs
+      - ../litellm_config.yaml:/app/config.yaml # Mount the local litellm_config.yaml file to the container
+      - ../logs/:/app/logs
     entrypoint: ["/bin/sh", "-c"]
     command:
       - >
@@ -124,7 +124,7 @@ services:
         --run_gunicorn
         --detailed_debug
         2>&1 | tee -a /app/logs/litellm.log
-    env_file: .env
+    env_file: ../.env
     ports:
       - "4000:4000" # Expose LiteLLM port to the host machine for direct access if needed, e.g. local dev
     networks:
@@ -154,7 +154,7 @@ services:
     ports:
       - "27017:27017"
     volumes:
-      - ./mongo-data:/data/db
+      - ../mongo-data:/data/db
     healthcheck:
       test: ["CMD", "healthchecks", "-s", "mongo"]
       interval: 35s
@@ -201,8 +201,8 @@ services:
       - DEV_MODE=1
       - CHAT_BOT=1
     volumes:
-      - ./docker/freva.conf:/data/evaluation_system.conf
-      - ./cache/:/opt/freva_web/static/preview/climateclaw
+      - ./freva.conf:/data/evaluation_system.conf
+      - ../cache/:/opt/freva_web/static/preview/climateclaw
 
   freva-cache:
     networks:
diff --git a/docker-compose.yml b/docker/docker-compose.yml
similarity index 91%
rename from docker-compose.yml
rename to docker/docker-compose.yml
index 74d8f35b..7ff9aa21 100644
--- a/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -2,9 +2,9 @@ services:
 
   climateclaw-base:
     # Build manually with:
-    # docker compose -f docker-compose.dev.yml --profile build-only build climateclaw-base
+    # docker compose -f docker/docker-compose.dev.yml --profile build-only build climateclaw-base
     build:
-      context: .
+      context: ..
       dockerfile: docker/Dockerfile.base
     image: ghcr.io/freva-org/climateclaw-base:latest
     profiles:
@@ -13,9 +13,9 @@ services:
   climateclaw:
     image: climateclaw-${CLIMATECLAW_INSTANCE_NAME:?Instance name must be set in the .env file to differentiate between instances}
     build:
-      context: .
+      context: ..
       dockerfile: docker/climateclaw/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: climateclaw-${CLIMATECLAW_INSTANCE_NAME}
     ports:
       - "${CLIMATECLAW_TARGET_PORT:-8502}:${CLIMATECLAW_BACKEND_PORT:-8502}" # If either is unset, the default value will be used.
@@ -40,9 +40,9 @@ services:
   code-server:
     image: code-server-${CLIMATECLAW_INSTANCE_NAME}
     build:
-      context: .
+      context: ..
       dockerfile: docker/code-server/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: code-server-${CLIMATECLAW_INSTANCE_NAME}
     environment:
       CLIMATECLAW_MCP_HOST: 0.0.0.0
@@ -64,9 +64,9 @@ services:
   web-search-server:
     image: web-search-server-${CLIMATECLAW_INSTANCE_NAME}
     build:
-      context: .
+      context: ..
       dockerfile: docker/web-search-server/Dockerfile
-    env_file: .env
+    env_file: ../.env
     hostname: web-search-server-${CLIMATECLAW_INSTANCE_NAME}
     environment:
       CLIMATECLAW_MCP_HOST: 0.0.0.0
@@ -86,7 +86,7 @@ services:
     image: ghcr.io/berriai/litellm:v1.102.0
     hostname: litellm-${CLIMATECLAW_INSTANCE_NAME}
     volumes:
-      - ./litellm_config.yaml:/app/config.yaml # Mount the local litellm_config.yaml file to the container
+      - ../litellm_config.yaml:/app/config.yaml # Mount the local litellm_config.yaml file to the container
       - /container/da/climateclaw-links/${CLIMATECLAW_INSTANCE_NAME}/logs:/app/logs
     entrypoint: ["/bin/sh", "-c"]
     command:
@@ -98,7 +98,7 @@ services:
         --run_gunicorn
         --detailed_debug
         2>&1 | tee -a /app/logs/litellm.log
-    env_file: .env
+    env_file: ../.env
     environment:
       CLIMATECLAW_VLLM_LITELLM_MODEL: "hosted_vllm/${CLIMATECLAW_VLLM_MODEL_ID:-nvidia/Gemma-4-31B-IT-NVFP4}"
     networks:
diff --git a/gen_compose.py b/docker/gen_compose.py
similarity index 97%
rename from gen_compose.py
rename to docker/gen_compose.py
index 5be2f52e..a0938699 100755
--- a/gen_compose.py
+++ b/docker/gen_compose.py
@@ -289,7 +289,7 @@ def generate_haproxy(
 def main():
 
     if len(sys.argv) < 2:
-        print("Usage: gen_compose.py docker-compose.dev.yml [project]")
+        print("Usage: docker/gen_compose.py docker/docker-compose.dev.yml [project]")
         sys.exit(1)
 
     compose_path = sys.argv[1]
@@ -373,7 +373,7 @@ def main():
     network_name = list(base["networks"].keys())[0]
 
     log_dir = (
-        "./logs/"
+        "../logs/"
         if "dev" in compose_path
         else "/container/da/climateclaw-links/${CLIMATECLAW_INSTANCE_NAME}/logs"
     )
@@ -421,9 +421,10 @@ def main():
         timeout=mcp_request_timeout,
     )
 
-    Path("haproxy.cfg").write_text(haproxy_cfg)
+    haproxy_path = input_path.with_name("haproxy.cfg")
+    haproxy_path.write_text(haproxy_cfg)
 
-    print(f"Generated {output_path.name} and haproxy.cfg")
+    print(f"Generated {output_path} and {haproxy_path}")
 
 
 if __name__ == "__main__":
diff --git a/prod.sh b/prod.sh
index 7792cc31..05a647b7 100755
--- a/prod.sh
+++ b/prod.sh
@@ -7,7 +7,7 @@ Usage: $(basename "$0") [OPTIONS] [COMPOSE_ARGS...]
 
 Deploy the climateclaw stack via podman-compose.
 
-Generates a scaled compose file from docker-compose.yml, tears down any
+Generates a scaled compose file from docker/docker-compose.yml, tears down any
 previous deployment, optionally rebuilds images, and starts the services.
 
 Options:
@@ -32,8 +32,8 @@ EOF
     exit 0
 }
 
-COMPOSE_FILE="docker-compose.yml"
-SCALED_FILE="docker-compose.scaled.yml"
+COMPOSE_FILE="docker/docker-compose.yml"
+SCALED_FILE="docker/docker-compose.scaled.yml"
 ENV_FILE=".env"
 PROJECT="${CLIMATECLAW_PROJECT_NAME:-}"
 do_build=false
@@ -122,7 +122,7 @@ fi
 # --- Generate scaled compose file ---
 echo "[prod.sh] Generating scaled compose file from ${COMPOSE_FILE}"
 echo "[prod.sh] Using project: ${CLIMATECLAW_PROJECT_NAME}"
-./gen_compose.py "${COMPOSE_FILE}" "${PROJECT}"
+./docker/gen_compose.py "${COMPOSE_FILE}" "${PROJECT}"
 
 # --- Tear down previous deployment ---
 ${COMPOSE} -f "${SCALED_FILE}" down
diff --git a/tests/unit_tests/test_gen_compose.py b/tests/unit_tests/test_gen_compose.py
index 26b6b6c8..3a83eb75 100644
--- a/tests/unit_tests/test_gen_compose.py
+++ b/tests/unit_tests/test_gen_compose.py
@@ -5,8 +5,8 @@
 import pytest
 import yaml
 
-# gen_compose.py is a repo-root script, while pytest only adds src/ to sys.path.
-GEN_COMPOSE_PATH = Path(__file__).resolve().parents[2] / "gen_compose.py"
+# gen_compose.py lives under docker/, while pytest only adds src/ to sys.path.
+GEN_COMPOSE_PATH = Path(__file__).resolve().parents[2] / "docker" / "gen_compose.py"
 spec = importlib.util.spec_from_file_location("gen_compose", GEN_COMPOSE_PATH)
 assert spec is not None
 assert spec.loader is not None
diff --git a/tests/unit_tests/test_prod_sh.py b/tests/unit_tests/test_prod_sh.py
index 7722d625..906014cb 100644
--- a/tests/unit_tests/test_prod_sh.py
+++ b/tests/unit_tests/test_prod_sh.py
@@ -12,8 +12,10 @@ def _prod_fixture(tmp_path, monkeypatch):
     repo_root = os.getcwd()
     shutil.copy(repo_root + "/prod.sh", tmp_path / "prod.sh")
     (tmp_path / "prod.sh").chmod(0o755)
-    (tmp_path / "docker-compose.yml").write_text("services: {}\n")
-    (tmp_path / "docker-compose.scaled.yml").write_text("services: {}\n")
+    docker_dir = tmp_path / "docker"
+    docker_dir.mkdir()
+    (docker_dir / "docker-compose.yml").write_text("services: {}\n")
+    (docker_dir / "docker-compose.scaled.yml").write_text("services: {}\n")
 
     bin_dir = tmp_path / "bin"
     bin_dir.mkdir()
@@ -29,7 +31,7 @@ def _prod_fixture(tmp_path, monkeypatch):
         "exit 0\n",
     )
     _write_executable(
-        tmp_path / "gen_compose.py",
+        docker_dir / "gen_compose.py",
         "#!/usr/bin/env bash\n"
         'echo "gen_compose $* PROJECT=$CLIMATECLAW_PROJECT_NAME"'
         ' >> "$PROD_SH_TEST_LOG"\n'
@@ -70,8 +72,14 @@ def test_prod_sh_project_flag_sets_project_and_uses_default_up_args(
     result = _run_prod(tmp_path, "--project", "codes")
 
     assert result.returncode == 0
-    assert "gen_compose docker-compose.yml codes PROJECT=codes" in log_path.read_text()
-    assert "podman-compose -f docker-compose.scaled.yml up -d" in log_path.read_text()
+    assert (
+        "gen_compose docker/docker-compose.yml codes PROJECT=codes"
+        in log_path.read_text()
+    )
+    assert (
+        "podman-compose -f docker/docker-compose.scaled.yml up -d"
+        in log_path.read_text()
+    )
 
 
 def test_prod_sh_project_equals_flag_sets_project(tmp_path, monkeypatch):
@@ -80,7 +88,10 @@ def test_prod_sh_project_equals_flag_sets_project(tmp_path, monkeypatch):
     result = _run_prod(tmp_path, "--project=codes")
 
     assert result.returncode == 0
-    assert "gen_compose docker-compose.yml codes PROJECT=codes" in log_path.read_text()
+    assert (
+        "gen_compose docker/docker-compose.yml codes PROJECT=codes"
+        in log_path.read_text()
+    )
 
 
 def test_prod_sh_reads_project_from_env_file(tmp_path, monkeypatch):
@@ -90,7 +101,10 @@ def test_prod_sh_reads_project_from_env_file(tmp_path, monkeypatch):
     result = _run_prod(tmp_path)
 
     assert result.returncode == 0
-    assert "gen_compose docker-compose.yml codes PROJECT=codes" in log_path.read_text()
+    assert (
+        "gen_compose docker/docker-compose.yml codes PROJECT=codes"
+        in log_path.read_text()
+    )
 
 
 def test_prod_sh_project_flag_overrides_env_file(tmp_path, monkeypatch):
@@ -100,7 +114,10 @@ def test_prod_sh_project_flag_overrides_env_file(tmp_path, monkeypatch):
     result = _run_prod(tmp_path, "--project", "codes")
 
     assert result.returncode == 0
-    assert "gen_compose docker-compose.yml codes PROJECT=codes" in log_path.read_text()
+    assert (
+        "gen_compose docker/docker-compose.yml codes PROJECT=codes"
+        in log_path.read_text()
+    )
 
 
 def test_prod_sh_preserves_compose_args_after_flags(tmp_path, monkeypatch):
@@ -110,5 +127,7 @@ def test_prod_sh_preserves_compose_args_after_flags(tmp_path, monkeypatch):
 
     assert result.returncode == 0
     log = log_path.read_text()
-    assert "podman-compose -f docker-compose.scaled.yml up --force-recreate" in log
+    assert (
+        "podman-compose -f docker/docker-compose.scaled.yml up --force-recreate" in log
+    )
     assert "--project codes" not in log

From 3d842e328a1498ec30227410117997d8920d0daf Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Fri, 2 Oct 2026 16:45:53 +0200
Subject: [PATCH 2/7] Anchor launcher scripts to repo root

---
 dev.sh  | 3 +++
 prod.sh | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/dev.sh b/dev.sh
index 09aecfa8..033a9e2a 100755
--- a/dev.sh
+++ b/dev.sh
@@ -1,6 +1,9 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
+ROOT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
+cd "${ROOT_DIR}"
+
 # ------------------------------------------------------------------
 # Simple dev launcher for ClimateClaw
 #
diff --git a/prod.sh b/prod.sh
index 05a647b7..67085faf 100755
--- a/prod.sh
+++ b/prod.sh
@@ -1,6 +1,9 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
+ROOT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
+cd "${ROOT_DIR}"
+
 usage() {
     cat <<EOF
 Usage: $(basename "$0") [OPTIONS] [COMPOSE_ARGS...]

From d588cce461e1afb1cd86d030b4551fe545ae119d Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Fri, 2 Oct 2026 16:57:22 +0200
Subject: [PATCH 3/7] Load root env file for relocated compose stacks

---
 .github/workflows/ci_job.yml     |  2 ++
 dev.sh                           |  7 ++++---
 docker/docker-compose.dev.yml    |  1 -
 prod.sh                          | 10 +++++-----
 tests/unit_tests/test_prod_sh.py |  5 +++--
 5 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci_job.yml b/.github/workflows/ci_job.yml
index a6c34bdb..98d5a39a 100644
--- a/.github/workflows/ci_job.yml
+++ b/.github/workflows/ci_job.yml
@@ -35,6 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       COMPOSE_FILE: docker/docker-compose.dev.yml
+      COMPOSE_ENV_FILES: .env
 
     steps:
       - name: Checkout
@@ -89,6 +90,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       COMPOSE_FILE: docker/docker-compose.yml
+      COMPOSE_ENV_FILES: .env
 
     steps:
       - name: Checkout
diff --git a/dev.sh b/dev.sh
index 033a9e2a..33d5e1d1 100755
--- a/dev.sh
+++ b/dev.sh
@@ -46,6 +46,7 @@ EOF
 export CLIMATECLAW_DEV=1
 
 CLIMATECLAW_DEBUG="${CLIMATECLAW_DEBUG:-0}"
+ENV_FILE=".env"
 COMPOSE_FILE="docker/docker-compose.dev.yml"
 BUILD_COMPOSE_FILE="${COMPOSE_FILE}"
 DO_BUILD=0
@@ -92,9 +93,9 @@ export CLIMATECLAW_DEBUG
 echo "[dev.sh] Using ${COMPOSE_FILE} with DEBUG=${CLIMATECLAW_DEBUG}"
 echo "[dev.sh] docker compose -f ${COMPOSE_FILE} ${COMPOSE_ARGS[*]}"
 
-docker compose -f "${BUILD_COMPOSE_FILE}" --profile build-only build climateclaw-base
+docker compose --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" --profile build-only build climateclaw-base
 if [ "${DO_BUILD}" = "1" ]; then
   echo "[dev.sh] Building images from ${BUILD_COMPOSE_FILE}"
-  docker compose -f "${BUILD_COMPOSE_FILE}" build
+  docker compose --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" build
 fi
-docker compose -f "${COMPOSE_FILE}" "${COMPOSE_ARGS[@]}"
+docker compose --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" "${COMPOSE_ARGS[@]}"
diff --git a/docker/docker-compose.dev.yml b/docker/docker-compose.dev.yml
index e583015e..71115213 100644
--- a/docker/docker-compose.dev.yml
+++ b/docker/docker-compose.dev.yml
@@ -122,7 +122,6 @@ services:
         --port=4000
         --num_workers=8
         --run_gunicorn
-        --detailed_debug
         2>&1 | tee -a /app/logs/litellm.log
     env_file: ../.env
     ports:
diff --git a/prod.sh b/prod.sh
index 67085faf..7e9348d7 100755
--- a/prod.sh
+++ b/prod.sh
@@ -128,19 +128,19 @@ echo "[prod.sh] Using project: ${CLIMATECLAW_PROJECT_NAME}"
 ./docker/gen_compose.py "${COMPOSE_FILE}" "${PROJECT}"
 
 # --- Tear down previous deployment ---
-${COMPOSE} -f "${SCALED_FILE}" down
+${COMPOSE} --env-file "${ENV_FILE}" -f "${SCALED_FILE}" down
 
 echo "[prod.sh] Building climateclaw-base from ${COMPOSE_FILE}"
-${COMPOSE} -f "${COMPOSE_FILE}" --profile build-only build climateclaw-base
+${COMPOSE} --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" --profile build-only build climateclaw-base
 
 if [ "$do_build" = true ]; then
     echo "[prod.sh] Building images ..."
-    ${COMPOSE} -f "${COMPOSE_FILE}" build
+    ${COMPOSE} --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" build
 fi
 
 # --- Start ---
 if [ ${#args[@]} -eq 0 ]; then
     args=(up -d)
 fi
-echo "[prod.sh] Starting: ${COMPOSE} -f ${SCALED_FILE} ${args[*]}"
-${COMPOSE} -f "${SCALED_FILE}" "${args[@]}"
+echo "[prod.sh] Starting: ${COMPOSE} --env-file ${ENV_FILE} -f ${SCALED_FILE} ${args[*]}"
+${COMPOSE} --env-file "${ENV_FILE}" -f "${SCALED_FILE}" "${args[@]}"
diff --git a/tests/unit_tests/test_prod_sh.py b/tests/unit_tests/test_prod_sh.py
index 906014cb..f8d02792 100644
--- a/tests/unit_tests/test_prod_sh.py
+++ b/tests/unit_tests/test_prod_sh.py
@@ -77,7 +77,7 @@ def test_prod_sh_project_flag_sets_project_and_uses_default_up_args(
         in log_path.read_text()
     )
     assert (
-        "podman-compose -f docker/docker-compose.scaled.yml up -d"
+        "podman-compose --env-file .env -f docker/docker-compose.scaled.yml up -d"
         in log_path.read_text()
     )
 
@@ -128,6 +128,7 @@ def test_prod_sh_preserves_compose_args_after_flags(tmp_path, monkeypatch):
     assert result.returncode == 0
     log = log_path.read_text()
     assert (
-        "podman-compose -f docker/docker-compose.scaled.yml up --force-recreate" in log
+        "podman-compose --env-file .env -f docker/docker-compose.scaled.yml up --force-recreate"
+        in log
     )
     assert "--project codes" not in log

From 78594894abd44cbafc1a1e7924e160174b22c298 Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Mon, 5 Oct 2026 16:25:48 +0200
Subject: [PATCH 4/7] Merge branch 'main' into reorganize-docker


From 63a68ec68a26695bf04b55f418bfe2adb51310ca Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Mon, 5 Oct 2026 16:31:23 +0200
Subject: [PATCH 5/7] Move ci compose to docker directory

---
 .github/workflows/ci_job.yml                          | 9 ++-------
 docker-compose.ci.yml => docker/docker-compose.ci.yml | 0
 2 files changed, 2 insertions(+), 7 deletions(-)
 rename docker-compose.ci.yml => docker/docker-compose.ci.yml (100%)

diff --git a/.github/workflows/ci_job.yml b/.github/workflows/ci_job.yml
index ee289887..d1c95215 100644
--- a/.github/workflows/ci_job.yml
+++ b/.github/workflows/ci_job.yml
@@ -89,7 +89,7 @@ jobs:
     name: Production smoke test
     runs-on: ubuntu-latest
     env:
-      COMPOSE_FILE: docker/docker-compose.yml
+      COMPOSE_FILE: docker/docker-compose.yml:docker/docker-compose.ci.yml
       COMPOSE_ENV_FILES: .env
 
     steps:
@@ -115,16 +115,11 @@ jobs:
 
       - name: Start production stack
         run: |
-          docker compose \
-            -f docker-compose.yml \
-            -f docker-compose.ci.yml \
-            up climateclaw code-server web-search-server \
+          docker compose up climateclaw code-server web-search-server \
             -d --wait --build --remove-orphans || {
               docker ps -a
 
               docker compose \
-                -f docker-compose.yml \
-                -f docker-compose.ci.yml \
                 logs climateclaw mongodb code-server web-search-server litellm
 
               exit 1
diff --git a/docker-compose.ci.yml b/docker/docker-compose.ci.yml
similarity index 100%
rename from docker-compose.ci.yml
rename to docker/docker-compose.ci.yml

From ef9c0c2bee938596765c2612feae8276f415328b Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Mon, 5 Oct 2026 17:50:09 +0200
Subject: [PATCH 6/7] Preserve repository-based compose project name in prod

---
 prod.sh                          | 12 +++++++-----
 tests/unit_tests/test_prod_sh.py |  9 ++++++---
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/prod.sh b/prod.sh
index 7e9348d7..e2d30f6b 100755
--- a/prod.sh
+++ b/prod.sh
@@ -3,6 +3,7 @@ set -euo pipefail
 
 ROOT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
 cd "${ROOT_DIR}"
+COMPOSE_PROJECT_NAME="${ROOT_DIR##*/}"
 
 usage() {
     cat <<EOF
@@ -125,22 +126,23 @@ fi
 # --- Generate scaled compose file ---
 echo "[prod.sh] Generating scaled compose file from ${COMPOSE_FILE}"
 echo "[prod.sh] Using project: ${CLIMATECLAW_PROJECT_NAME}"
+echo "[prod.sh] Using Compose project: ${COMPOSE_PROJECT_NAME}"
 ./docker/gen_compose.py "${COMPOSE_FILE}" "${PROJECT}"
 
 # --- Tear down previous deployment ---
-${COMPOSE} --env-file "${ENV_FILE}" -f "${SCALED_FILE}" down
+${COMPOSE} --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${SCALED_FILE}" down
 
 echo "[prod.sh] Building climateclaw-base from ${COMPOSE_FILE}"
-${COMPOSE} --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" --profile build-only build climateclaw-base
+${COMPOSE} --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" --profile build-only build climateclaw-base
 
 if [ "$do_build" = true ]; then
     echo "[prod.sh] Building images ..."
-    ${COMPOSE} --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" build
+    ${COMPOSE} --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" build
 fi
 
 # --- Start ---
 if [ ${#args[@]} -eq 0 ]; then
     args=(up -d)
 fi
-echo "[prod.sh] Starting: ${COMPOSE} --env-file ${ENV_FILE} -f ${SCALED_FILE} ${args[*]}"
-${COMPOSE} --env-file "${ENV_FILE}" -f "${SCALED_FILE}" "${args[@]}"
+echo "[prod.sh] Starting: ${COMPOSE} --project-name ${COMPOSE_PROJECT_NAME} --env-file ${ENV_FILE} -f ${SCALED_FILE} ${args[*]}"
+${COMPOSE} --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${SCALED_FILE}" "${args[@]}"
diff --git a/tests/unit_tests/test_prod_sh.py b/tests/unit_tests/test_prod_sh.py
index f8d02792..9a6a1954 100644
--- a/tests/unit_tests/test_prod_sh.py
+++ b/tests/unit_tests/test_prod_sh.py
@@ -77,7 +77,9 @@ def test_prod_sh_project_flag_sets_project_and_uses_default_up_args(
         in log_path.read_text()
     )
     assert (
-        "podman-compose --env-file .env -f docker/docker-compose.scaled.yml up -d"
+        "podman-compose "
+        f"--project-name {tmp_path.name} "
+        "--env-file .env -f docker/docker-compose.scaled.yml up -d"
         in log_path.read_text()
     )
 
@@ -128,7 +130,8 @@ def test_prod_sh_preserves_compose_args_after_flags(tmp_path, monkeypatch):
     assert result.returncode == 0
     log = log_path.read_text()
     assert (
-        "podman-compose --env-file .env -f docker/docker-compose.scaled.yml up --force-recreate"
-        in log
+        "podman-compose "
+        f"--project-name {tmp_path.name} "
+        "--env-file .env -f docker/docker-compose.scaled.yml up --force-recreate" in log
     )
     assert "--project codes" not in log

From 209f76a288db44a9e75f2bde1a16588cad0a3d70 Mon Sep 17 00:00:00 2001
From: Gizem Ekinci <ekinci@dkrz.de>
Date: Mon, 5 Oct 2026 18:09:56 +0200
Subject: [PATCH 7/7] Preserve repository-based compose project name in dev

---
 dev.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/dev.sh b/dev.sh
index d526fed1..9f99d284 100755
--- a/dev.sh
+++ b/dev.sh
@@ -3,6 +3,7 @@ set -euo pipefail
 
 ROOT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
 cd "${ROOT_DIR}"
+COMPOSE_PROJECT_NAME="${ROOT_DIR##*/}"
 
 # ------------------------------------------------------------------
 # Simple dev launcher for ClimateClaw
@@ -94,9 +95,9 @@ export CLIMATECLAW_DEBUG
 echo "[dev.sh] Using ${COMPOSE_FILE} with DEBUG=${CLIMATECLAW_DEBUG}"
 echo "[dev.sh] docker compose -f ${COMPOSE_FILE} ${COMPOSE_ARGS[*]}"
 
-docker compose --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" --profile build-only build climateclaw-base
+docker compose --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" --profile build-only build climateclaw-base
 if [ "${DO_BUILD}" = "1" ]; then
   echo "[dev.sh] Building images from ${BUILD_COMPOSE_FILE}"
-  docker compose --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" build
+  docker compose --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${BUILD_COMPOSE_FILE}" build
 fi
-docker compose --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" "${COMPOSE_ARGS[@]}"
+docker compose --project-name "${COMPOSE_PROJECT_NAME}" --env-file "${ENV_FILE}" -f "${COMPOSE_FILE}" "${COMPOSE_ARGS[@]}"