I was expecting to be able to control the output folder entirely.

In my use case, I was thinking of putting multiple altdoc-managed packages into a single mkdocs website. So, I'll already have a parent docs folder; I want to control the name of the subfolder I put this particular package's docs in.

Ok so you'd expect ../mydocs to contain the documentation files. But until #298 is solved I don't think you'd be able to have those multiple subfolders with each containing a separate altdoc documentation. Even if it was solved, each subfolder would still contain an mkdocs.yml file, so for instance you might have:

• all-docs
  • pkgA-docs
    • mkdocs.yml
    • other files...
  • pkgB-docs
    • mkdocs.yml
    • other files...

Would mkdocs still work with this structure? I've never made multi-project websites.

Well, I would put the primary mkdocs config under all-docs.
Then mkdocs would just ignore the other ones. So, they could be deleted/ignored/whatever, and I think it could work.

Is altdoc simply copying the mkdocs.yml file over from the altdoc/ folder in the R package?
If so, possibly a setting like include_mkdocs_config=FALSE or suppress_mkdocs_config=TRUE could just prevent it from creating it.

Is altdoc simply copying the mkdocs.yml file over from the altdoc/ folder in the R package?

It copies the file but also replaces some template variable e.g. $ALTDOC_PACKAGE_VERSION, by their actual values.

If so, possibly a setting like include_mkdocs_config=FALSE or suppress_mkdocs_config=TRUE could just prevent it from creating it.

I don't want to add arguments that are tool-specific. This would only be useful for mkdocs and not for the others. I'd prefer you to delete those files yourself after generating all the package doc subfolders in your main "all-docs" folder, as you suggested.

Could you try this PR, just to check that the structure of output is as you expect? (I know #298 is still the main issue here)