* 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
* Wrote functional tests for desired behavior.
Redoing the pull request, starting from current master.
The tests now fail where expected.
* Updated commands to handle missing files better.
The functional tests now pass.
