Cleanup bash

Cleans up inline bash scripts from yaml files and puts them into distinct shell scripts that are then called from yaml.

• Move scripts into new files using -before and -run as suffix for before scripts and scripts
• Test each stage in pipeline with changes
• Add set -euo pipefail to shell scripts
• Test force pipeline fail if exit code from shell script is non-zero
• Remove sh and source from yaml files
• Make shell scripts executable
• Combine before scripts with run scripts
• Quote all environment vars

Issue is located here