move to subdirectory and add measurements

Dockerfile

+# glpk also from https://github.com/dmccloskey/glpk/blob/master/Dockerfile
+
+# Set the base image to Ubuntu
+FROM ubuntu:latest
+# Switch to root for install
+USER root
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV HOME /home/user
+RUN useradd --create-home --home-dir $HOME user \
+    && chmod -R u+rwx $HOME \
+    && chown -R user:user $HOME
+
+RUN apt-get update -y && apt-get install -y \
+	openjdk-8-jdk \
+	r-base \
+	r-base-dev \
+	libudunits2-dev \
+	cowsay \
+	less \
+	--no-install-recommends \
+	&& apt-get clean \
+	&& rm -rf /var/lib/apt/lists/*
+
+COPY trainbenchmark-reporting/install.R /trainbenchmark/trainbenchmark-reporting/install.R
+RUN Rscript /trainbenchmark/trainbenchmark-reporting/install.R
+
+#USER user
+WORKDIR /trainbenchmark
+
+COPY --chown=user:user . .
+COPY docker/bashrc /home/user/.bashrc
+
+RUN ./gradlew --no-daemon preprocess
+RUN ./gradlew --no-daemon build shadowJar -x test
+RUN ./gradlew --no-daemon initScripts
+
+
+
+# when benchmarking run:
+# RUN ./gradlew --no-daemon generate
+# RUN ./gradlew --no-daemon individualInjectBenchmark
+# RUN ./gradlew --no-daemon individualRepairBenchmark
+ENTRYPOINT /bin/bash