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It looks like the archive which was created contains a submodule reference. Which is annoying because the archive is supposed to be free of any vcs related files.

I don't think bloom can support this unless git archive ... also exports and flattens any submodule contents...

Currently I use vcstools to do an vcs agnostic "archive", which calls the correct vcs command based on the vcs being used. So bloom doesn't interact with the upstream directly ever. But since the .gitmodules file persists with the archive it is breaking things...

Can you open a ticket against bloom?

For now I would say submodules are not supported, at least until I figure out what needs to be done to support them correctly.