* documentation and script updates trying to fix#1647
* preparations for refactoring target/bin/
* complete refactor for target/bin/
* changing script output slightly
* outsourcing functions in `bin-helper.sh`
* re-wrote linting to allow for proper shellcheck -x execution
* show explanation for shellcheck ignore
* adding some more information
Added optional FQDN arguement to setup.sh script which avoids using temporary container hostname for cert names. Also fixed issue with certs being saved outside config volume