My dotfiles repository has some tmux plugin directories which are themselves git repositories. When I do git add -all these nested repos are ignored.
Is there a way to ignore the git semantics of these nested repos and treat everything as regular files?
You may be looking for the Git feature called submodules. This
feature helps you manage dependent repositories that are nested inside
your main repository.
Answer from here
Also you might want to check the .gitignore files you might have. It can prevent the nested repositories from being added.