Resolve "Address Pylama and Shellcheck findings"

Closes #285 (closed) Closes #294 (closed)

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

In addition to resolving outstanding shellcheck and pylama findings in the development branch, this MR:

1. Fixed a bug where some shell scripts were not being scanned with shellcheck because of their directory depth.
2. Fixed a bug where the shellcheck stage 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.
3. Skip scripts/analysis directory in shellcheck and pylama stages
4. Remove allow-failure and related comments from shellcheck and pylama stages.