Fix agent rollback does not delete created dirs

[Dean-Coakley]

Bug

If a config was pushed which caused a rollback on apply. The rollback function would not removing any directories it created during the config apply.

Proposed changes

• Marks directories created on config apply so they can be removed on rollback if required.

Checklist

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• I have read the CONTRIBUTING document
• If applicable, I have added tests that prove my fix is effective or that my feature works
• If applicable, I have checked that any relevant tests pass after adding my changes
• I have updated any relevant documentation (README.md)