Resolve "Address Shellcheck findings"

Closes #294 (closed)

See ticket for before/after testing notes. See commit messages for notes on each finding's cause and/or resolution.

In addition to resolving outstanding shellcheck findings in the devleopment branch, this MR fixes two bugs in the shellcheck stage.

1. Some shell scripts were not being scanned because of their directory depth.
2. The return value was reset to zero before scanning embedded scripts. This would resulting in a passing shellcheck stage if there were no findings in embedded scripts but there were findings in shell scripts.