- 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.
