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Submodules are marked as dirty in the staging view of the super project if - the Submodule Link in the super project does not match the HEAD commit of the submodule or - the submodule itself is dirty (git status describes this case as "modified content") In the first case the change can be added and committed inside the super project. In the second case the change can **not** be added and committed inside the super project. Therefore I suggest to render the second change differently. Some ideas: - other decorator - other color (greyed out?) - new area in the Staging View