- Add sophisticated file preservation functionality to _clean_output_dir()
- Support .qsgen3_preserve file with shell glob patterns for selective preservation
- Preserve shared articles and important files during site regeneration
- Maintain backward compatibility (no preserve file = complete cleaning)
- Add comprehensive documentation in how-it-works.md
- Include example preserve file (.qsgen3_preserve.example)
- Remove legacy images directory and update documentation
- Fix workflow documentation formatting issues
- Implement flexible theme switching via site.conf (site_theme, site_theme_css_file).
- Ensure correct copying of theme static assets, with theme assets overriding root assets.
- Resolve CSS linking issues by checking file existence after static copy and using correct paths for Pandoc.
- Refactor path construction to prevent duplication when using absolute/relative output paths.
- Create comprehensive how-it-works.md detailing system architecture, theme creation, and overall workflow.
- Clarify design philosophy: qsgen3 remains design-agnostic, only linking main theme CSS automatically.
