publishing to a sub-directory

[KolyaKorruptis]

I already have a github pages site, which I didn't want to replace with the output of this plugin.
So I created a new repository for it which now gets published at www.my-existing-site.com/notes

However it seems the plugin cannot deal with output not being in the root folder. It now looks for the archives page at:
www.my-existing-site.com/archives
whereas it should be looking for:
www.my-existing-site.com/notes/archives

And the same for all other pages and assets.

How can I tell the plugin that the content is in a sub directory?