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SmartGit shows the repository status in the Directories pane view. If the submodule's current state does not exactly correspond to the state defined by .gitsvnextmodules (same URL, revisions, ...), it will show ups as modified. In this case, can use Local|Stage to update the .gitsvnextmodules configuration to the current SVN submodule state or you can use Remote|Submodule|Reset to put the submodule back into the state as it is registered in .gitsvnextmodules.

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