In a current project I’m using Pkg.add(url="url/to/pkg", subdir = "in/this/subdir") . Now with 1.11 there is a [sources] section of the Project.toml file that makes this approach just a little bit nicer (e.g. I can delete the Manifest.toml without having to using Pkg.add again).
However, it appears that the subdir kwarg is not replicated in the source specification.
e.g.