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This is quite a specific bug, but one that should be resolved so that others are my workplace will have the confidence to know SourceGit can properly support submodules!
So what happened was that made a fresh clone of a remote repo that had various submodules. One of those submodules my account did not have permission to access, leading to a "submodule not found at..." error. The project then didn't open, so I opened it locally. I then clicked on the Update all submodules button on the left, and upon opening each submodule in a new tab, each and every one of them had all of their files deleted and with those deletion actions already staged.
Of course, I could solve this by unstaging, then discarding all the deletions thankfully, but this issue made my boss at work think that SourceGit did not support Submodules properly and he switch back immediately to SourceTree :( So I would very much like this strange auto delete and stage issues to be resolved! I'm not sure if you need to have a submodule you don't have permission to access to trigger this bug, but these were my repro steps anyways.