I asked several months ago for an addition to Jekyll core that would enable users to specify the order of collection items via _config.yml. A volunteer prepared a PR (see https://github.com/jekyll/jekyll/pull/5904) and I'd be grateful if someone could let us know whether it's likely to be merged some time soon.
Use case: we are using GitHub Pages to build lessons for Software Carpentry and other groups. The lesson sections are in a collection; to order them, we currently have to use naming (like 01-intro.md, 02-basics.md, etc.), but this makes it painful to re-order things (multiple filenames need to change, internal links need to be altered, etc.). Setting the order in _config.yml, and having the previous/next links set up to respect this order automatically, would make life a lot easier.
Constraint: we want to be able to render on GitHub, which means we can't use plugins, which means we need this in core.