diff --git a/.github/workflows/deploy-docker.yaml b/.github/workflows/deploy-docker.yaml
index 65d0bd4bb6..b62aeba4eb 100644
--- a/.github/workflows/deploy-docker.yaml
+++ b/.github/workflows/deploy-docker.yaml
@@ -17,7 +17,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           lfs: false
-          submodules: false
+          submodules: true
 
       - name: Do pull to ensure up-to-date
         run: git pull
diff --git a/modules/benchmark b/modules/benchmark
index 1a7ac8d0b5..06f84c75be 160000
--- a/modules/benchmark
+++ b/modules/benchmark
@@ -1 +1 @@
-Subproject commit 1a7ac8d0b59c6b0837253ab60e1de703ab015456
+Subproject commit 06f84c75bee0726f7bb010617e6d8dd8a04190d3
diff --git a/modules/cli b/modules/cli
index b1df5ae454..6a4c41e617 160000
--- a/modules/cli
+++ b/modules/cli
@@ -1 +1 @@
-Subproject commit b1df5ae4543d9dd8d28fed46f0b477a4441fa9e6
+Subproject commit 6a4c41e6171beee1dfdf9ffefa431713be495da7
diff --git a/modules/statistics b/modules/statistics
index 355411e920..d19b5c618f 160000
--- a/modules/statistics
+++ b/modules/statistics
@@ -1 +1 @@
-Subproject commit 355411e920631afdea91ccf47982a35615e7b04b
+Subproject commit d19b5c618f844bfcd05e7c26e08f282393fd332a
diff --git a/package-lock.json b/package-lock.json
index 586fd21c78..e96ee2d9b4 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -7,7 +7,6 @@
     "": {
       "name": "@eagleoutice/flowr",
       "version": "1.5.0",
-      "hasInstallScript": true,
       "license": "ISC",
       "dependencies": {
         "@types/semver": "^7.5.6",
diff --git a/package.json b/package.json
index e5545c2a1a..8d04efe5ab 100644
--- a/package.json
+++ b/package.json
@@ -74,43 +74,43 @@
         {
           "zones": [
             {
-              "target": "benchmark",
+              "target": "modules/benchmark",
               "from": [
-                "cli",
+                "modules/cli",
                 "src",
-                "statistics"
+                "modules/statistics"
               ]
             },
             {
-              "target": "cli",
+              "target": "modules/cli",
               "from": [
-                "benchmark",
+                "modules/benchmark",
                 "src",
-                "statistics"
+                "modules/statistics"
               ]
             },
             {
-              "target": "statistics",
+              "target": "modules/statistics",
               "from": [
-                "benchmark",
-                "cli",
+                "modules/benchmark",
+                "modules/cli",
                 "src"
               ]
             },
             {
               "target": "src",
               "from": [
-                "benchmark",
-                "cli",
-                "statistics"
+                "modules/benchmark",
+                "modules/cli",
+                "modules/statistics"
               ]
             },
             {
               "target": "test",
               "from": [
-                "benchmark",
-                "cli",
-                "statistics"
+                "modules/benchmark",
+                "modules/cli",
+                "modules/statistics"
               ]
             }
           ]
diff --git a/scripts/Dockerfile b/scripts/Dockerfile
index b1b6c5fc94..dca66d8b58 100644
--- a/scripts/Dockerfile
+++ b/scripts/Dockerfile
@@ -4,11 +4,18 @@ FROM node:21.4-alpine3.19 AS builder
 
 WORKDIR /app
 
+# copy all modules into the workdir
 COPY ./src /app/src/
 COPY ./package.json ./package-lock.json ./tsconfig.json /app/
+COPY ./modules/benchmark /app/modules/benchmark
+COPY ./modules/cli /app/modules/cli
+COPY ./modules/statistics /app/modules/statistics
 
-RUN npm install
-RUN npm run build
+# install and build all modules
+RUN npm install && npm run build
+RUN cd modules/benchmark && npm install && npm run build
+RUN cd modules/cli && npm install && npm run build
+RUN cd modules/statistics && npm install && npm run build
 
 
 FROM node:21.4-alpine3.19 AS flowR
@@ -19,11 +26,26 @@ WORKDIR /app
 
 RUN apk add --no-cache R
 
-# we keep the package.json for module resolution
-COPY ./package.json ./scripts/demo.R LICENSE /app/
+COPY ./scripts/demo.R LICENSE /app/
+
+# copy all package.jsons so we can install them (see below)
+COPY ./package.json /app/
+COPY ./modules/benchmark/package.json /app/modules/benchmark/
+COPY ./modules/cli/package.json /app/modules/cli/
+COPY ./modules/statistics/package.json /app/modules/statistics/
+
+# install all modules so that we have dependencies in here too
+# (we don't copy them from the builder because builder modules include dev deps too)
 RUN npm install --omit=dev
+RUN cd modules/benchmark && npm install --omit=dev
+RUN cd modules/cli && npm install --omit=dev
+RUN cd modules/statistics && npm install --omit=dev
 
 COPY --from=builder /app/dist/src /app/dist
-RUN rm -rf /app/dist/tsconfig.tsbuildinfo
+COPY --from=builder /app/modules/benchmark/dist /app/modules/benchmark/dist
+COPY --from=builder /app/modules/cli/dist/src /app/modules/cli/dist
+COPY --from=builder /app/modules/statistics/dist /app/modules/statistics/dist
+
+RUN rm -rf /app/**/tsconfig.tsbuildinfo
 
-ENTRYPOINT ["node", "/app/dist/flowr.js"]
+ENTRYPOINT ["node", "/app/modules/cli/dist/flowr.js"]
diff --git a/tsconfig.json b/tsconfig.json
index 84c50230b3..e799db8d72 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -16,8 +16,6 @@
   "exclude": [
     "node_modules/**/*",
     "dist/**/*",
-    "cli",
-    "benchmark",
-    "statistics"
+    "modules/**/*"
   ]
 }