Clean up scripts used for the old manuscript

[nikosbosse]

Description

This PR closes #881

This PR removes the manuscript/R folder that held the scripts used to generate figures for the old manuscript. Scripts for those figures have been fixed moved to issues. The idea was that we could use some of the visualisations in different contexts again (e.g. vignettes) in the future.
Code for the only figure that is still included in the current manuscript has been moved directly to the manuscript.Rmd file.

Checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have included the target issue or issues in the PR title as follows: issue-number: PR title
• I have tested my changes locally.
• I have added or updated unit tests where necessary.
• I have updated the documentation if required.
• I have built the package locally and run rebuilt docs using roxygen2.
• My code follows the established coding standards and I have run lintr::lint_package() to check for style issues introduced by my changes.
• I have added a news item linked to this PR.
• I have reviewed CI checks for this PR and addressed them as far as I am able.

[seabbs]

Good idea