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I haven't been having issues with this and I've been switching between branches with a lot of work-in-progress. Many times I find that a submodule exists in one branch but not in another. To make sure I can build I run git submodule update --init --recursive ./SUBMODULE_DIR after I check out a change.
@nateinaction with a bit of wrenching this might be an upstream GitHub Desktop issue? When I use the command line everything is fine. Perhaps the way we are setting up the submodules is not agreeing with the way GitHub Desktop wants to pull things in?
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