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Sourcetree moving my lfs and hooks files to root of repo?

I've been having a few ongoing issues with sourcetree. It continuously moves my lfs and hooks files out of my git folder and into the root of the repo. This I believe is causing my external merge tool to not work. I also have problems when trying to push with the branches not being displayed, so I have to keep closing the window and reopening it, or sometimes uncommitted changes won't show up unless I close and reopen sourcetree. I have no idea if these problems are related or not. Anyone else see these problems? Any ideas how to fix?

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