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Consider this project layout: project (top-level repo) src (linked folder) nested1 (nested repo) file.txt Making a change to file.txt and saving it neither results in a "dirty" decoration nor does it result in the file.txt being shown as an unstaged change in the Git Staging view. Bad. The change is detected if the workbench is restarted. If I were to guess the resource delta is dropped on the floor when a file is in a subtree rooted at a linked resource ignoring the fact there is a repo below it.