Refactor Package structure

This commit cleans up the package structure, to make two new top-level
packages `internal` (for internal-use packages) and `pkg` (for general
shared utility code).

internal/component/triplestore/stack/Dockerfile

@@ -0,0 +1,64 @@
+# This Dockerfile contains instructions to compile and run GraphDB inside a Docker container. 
+# It is roughly based on https://github.com/Ontotext-AD/graphdb-docker/blob/master/free-edition/Dockerfile
+# but has been modified for performance and security. 
+
+# This image is intended to be built like:
+#   docker build --build-arg graphdb_src=graphdb.zip .
+
+# We first make a base image to base further builds on. 
+# We don't use alpine here, as that uses significantly slower musl instead of glibc. 
+FROM adoptopenjdk/openjdk11:debian-slim as base
+
+# Create a user called graphdb
+RUN useradd -ms /bin/bash graphdb
+
+# make a base images, to add the sources to. 
+FROM base as sources
+
+# install unzip
+RUN apt-get update && apt-get install -y unzip
+
+# add the source file (by default graphdb.zip) to the image
+ARG src=graphdb.zip
+ADD ${src} /graphdb.zip
+
+# unpack it into a temporary directory
+RUN unzip "$src" -d "/unpack/"
+
+# Move it into /opt/graphdb, and chown it to graphdb
+RUN mv "/unpack"/* /opt/graphdb
+RUN chown -R graphdb:graphdb /opt/graphdb
+
+# finally make an image that will run
+FROM base as final
+
+# add the entrypoint script
+ADD entrypoint.sh /entrypoint.sh
+
+# copy over the sources
+COPY --from=sources /opt/graphdb /opt/graphdb
+
+# set environment variables for graphdb_home and path
+ENV GRAPHDB_HOME=/opt/graphdb
+ENV PATH=$GRAPHDB_HOME/bin:$PATH
+
+# Workaround for CVE-2021-44228 
+# (not sure if we are vulnerable, but just because)
+ENV LOG4J_FORMAT_MSG_NO_LOOKUPS=true
+
+# expose a port
+EXPOSE 7200
+
+# setup a healthcheck, that checks if the server is up. 
+RUN apt-get update && apt-get install -y curl
+HEALTHCHECK --interval=30s --timeout=30s --start-period=5s --retries=3 CMD curl --fail 127.0.0.1:7200/rest/repositories || exit 1
+
+# Add volumes for data, work and logs as these might be accessible from the outside. 
+# To add your own configuration, manually mount a config file into /opt/graphdb/work
+VOLUME /opt/graphdb/data
+VOLUME /opt/graphdb/work
+VOLUME /opt/graphdb/logs
+
+# setup command and entrypoint
+CMD ["-Dgraphdb.home=/opt/graphdb"]
+ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]