Structure and filenames of code files no longer match page URLs - fix that

[sharon-tickell]

As a result of all the refactoring in May 2025, many of the code-filenames and the directory structure they are in no longer match the URLs that the content of those pages is available at. This should be fixed to avoid confusion for future team members updating the site.

• tools.md should be renamed to outputs.md to match the change of name of that page.
• The research/publications subdirectory should probably be just an 'outputs subdirectory

And we should review whether the URLs for markdown pages should have .html extension or not, as we're a bit inconsistent there.