Which I guess makes the confusion complete, I guess …
I would say this:but
Submodules is, in most cases, your best choice. You can easily pull in updated theme(s) when needed.
Assuming your project is already a git project, then git clone sounds a little weird, and we should probably fix that. It may be a good option if your site isn’t a Git project. I.e. git clone some theme and then delete .git folder. Maybe also if you plan to use a theme as a starting point and never intend to synch in changes from the source.
The reasons why we use sub tree in the docs site is mainly:
We have a “mirror” of the docs in the main Hugo project (below /docs), so /docs is a subtree with the theme as another subtree …
Ready to build (hugo server) documentation is with this automatically packaged as part of the source distribution when we release, including theme and all.
We can also add documentation changes as part of the code changes in the same PRs if we need to.
I’m just starting out with Hugo and read the quickstart and then theme docs, was a bit confused about which is the best path to follow, so would probably help beginners to have it consistent in documentation