Documentation TODOs

[dilpath]

• correct the whitespace in tables from the markdown->RST conversion.
• correct the links in format.rst
• read over all documentation and check for consistency with new format decisions
• store tables outside RST for maintainability, e.g. like https://github.com/PEtab-dev/PEtab/tree/main/doc/src
• delete outdated /docs directory with old markdown docs
• move docs for "hybridization types" out of the "hybridization table", since the type is not defined in the table, but rather the PEtab YAML extension section.
• fix "tip" boxes in format.rst
• remove old docs directory
• update README and repo short description to point to docs