- Restructured 'minimal' theme to use 'static/css' and 'static/js' subdirectories for assets, aligning with qsgen3's expected theme structure.
- Moved 'minimaltemplate-v1.css' to 'themes/minimal/static/css/'.
- Moved JS files from 'themes/minimal/css/' to 'themes/minimal/static/js/'.
- Updated 'site.conf.example' to reflect 'minimal' theme usage and correct 'site_theme_css_file' path relative to the theme's static directory.
- Cleaned up redundant CSS variable definitions in 'bin/qsgen3' (_generate_index_page function).
- 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.
