Add a table of content to the README file

Since the README file is becoming increasingly larger, it seems convenient to add a table of contents. This MR intends to do so.

I also brought some minor changes:

• There was a duplicate Prerequisites section at the end. I deleted it.
• I renamed the subcommand subsection titles with the explicit subcommand
• I used a Vim plugin to generate the table of contents (TOC) automatically. It adds tags before and after the TOC to make it easier to update it.