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Consolidate documentation from PRs #220 and #433 into a new structured docs layout following the bfabric core docs pattern. New sections: - getting_started/: installation, quick start (Makefile workflow), configuration - user_guides/: deploying apps, creating apps, inputs, outputs, CLI reference, Python environments - api_reference/: autodoc index for key specs and models - resources/: links to changelog, repo, and bfabricPy docs Updated: - conf.py: sphinx_book_theme, MyST extensions, autodoc_pydantic - architecture/overview.md: narrative text for workflow phases and components - specs/app_specification.md: added CommandShell and CommandPythonEnv sections - specs/output_specification.md: added bfabric_link example, fixed CLI usage
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there were some earlier efforst in #220 which should be merged into this branch as well