📚 docs(README.md): update table of contents and headings for better organization and readability

🔧 chore(README.md): reformat and update CLI section for clarity and consistency
The README.md file has been updated to improve the organization and readability of the document. The table of contents has been updated to include all relevant sections. Headings have been adjusted to provide a clear hierarchy and improve navigation. The CLI section has been reformatted and updated to provide clearer instructions and explanations.