Release v0.1.3: document the codon usage and repeat analysis toolkits

- README: add a "What's new in v0.1.3" section and refresh the feature
  list, repository structure, module tables, usage examples and citation
- CHANGELOG: add the 0.1.3 entry and update the comparison links
- CITATION.cff: bump version to 0.1.3, update the release date, abstract
  and keywords
- Update the module index READMEs (analyzer, Plots, Plots/Codon_plot,
  Plots/Codon_plot/GC12_GC3, Seqtool, other_tools) to cover the new tools
- Add the analyzer/misa_tool index README that was lost when misa_parser
  was moved into its own sub-directory
