Add custom exceptions

[ArBridgeman]

Summary

With the tbx workflow update, we can modify 1 or more files. Each of these files goes through multiple steps. To reduce headaches later, we should introduce custom exception to make it clear what the step the exception relates to and what should be checked.

Also, as a stepping stone, it's useful if we add extract_by_workflow and refactor how the YamlRender classes behave.