This uses pandoc to enable generating pdf from markdown, with latex intertwined.
To build the report, I am using the docker image pandocglossaries:1.0 created by the Dockerfile in this repository. To build, run the run_docker.sh script. Remember to first give it permission to run. The index.txt is where the order of the files in section are added.
This includes a filter that makes it easier to use glossaries from latex. More info here
To add packages, they need to be added in the Dockerfile, and rebuilt.