Convert the single-animal user guide to MyST-friendly markdown and improve layout and clarity. Changes include: add a table-of-contents directive; replace raw HTML <img>/<p> blocks with MyST image directives and metadata; introduce admonitions (important/note/caution/hint) for critical points; restructure the project directory section into bulleted lists and an ASCII tree; clarify Windows path guidance and config.yaml parameter notes; normalize API Docs headings and other formatting fixes. These are documentation/formatting updates to improve rendering and readability—no functional code changes.