One repo contains the Hugo content and themes files. The other contains the generated site. The former contains the latter as a submodule.
When a post is renamed or removed between site generations, unwanted files can be left behind in the generated site directory. To eliminate this problem,
hugo --cleanDestinationDir will remove any extraneous files and folders from the destination folder, except for folders that begin with
. (hidden folders). This behavior was added to avoid removing
.git/ folders. Unfortunately, git submodules contain a
.git file, and will be removed when using
--cleanDestinationDir (as well as any other hidden files, like
There is an open (ignored) PR to fix this for the
.git file. However,
.gitignore would still be removed. To handle this, they'd need to add yet another exception for this file or expose yet another configuration parameter to allow the user to define which files to preserve. Both solutions are entering the “bloat” realm, so we're unlikely to see the change made.
As a workaround, all hidden files and folders can be ignored by modifying the
deploy.sh bash script that is provided by Hugo in their documentation for Github Pages deployment.