Documentation TODOs

• 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• delete outdated /docs directory with old markdown docs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

Review the remaining unchecked task and compare the current RST documentation with the table organization in the linked PEtab example. Start with the documentation files referenced in the checklist, including format.rst and README, and verify that tables are maintained outside RST while the documentation links and descriptions remain consistent.