Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
Eric Coissac