hotfix: apply CLI flags to entire subtree

[zivkovicmilos]

Description

As pointed out in #555, the current command flag registration flow does not register flags with grandchild commands, and beyond.
This PR introduces a fix for allowing the most nested child commands to have flags of their entire ancestor tree.

Changes include

• Bugfix (non-breaking change that solves an issue)
• Hotfix (change that solves an urgent issue, and requires immediate attention)
• New feature (non-breaking change that adds functionality)
• Breaking change (change that is not backwards-compatible and/or changes current functionality)

Checklist (for contributors)

• I have assigned this PR to myself
• I have added at least 1 reviewer
• I have added the relevant labels
• I have updated the official documentation
• I have added sufficient documentation in code

Testing

• I have tested this code with the official test suite
• I have tested this code manually

Manual tests

• Manually verified that the issue has been resolved
• Added unit tests that covered the issue functionality

Additional comments

Resolves #555

[faddat]

I really enjoyed the linting.