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Restructure report/unit modules and add CLI logging/output options#3

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pixge wants to merge 24 commits into
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Restructure report/unit modules and add CLI logging/output options#3
pixge wants to merge 24 commits into
codex/create-project-skeleton-with-ast-scanner-lrhe9cfrom
codex/modify-scaffolding-and-implement-logging

Adds prompts for code writing and refactoring

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