Just to clarify, something like this is what I meant:
├── site-foo
│ ├── config
│ │ ├── _default
│ │ ├── development
│ │ └── production
│ └── ...
└── themes
├── theme1
└── theme2
# dev
themesDir = "../../themes"
theme = "theme1"
# prod
theme = "github.com/pointyfar/theme1"
I do not use git submodules.