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I think you've answered the question yourself: it doesn't work.
Using git submodules requires extra submodule init and checkout steps that probably don't happen anywhere along the release pipeline.
Working with git submodules tends to be tricky and error-prone, and most of the developers I've met do their best to stay away from them.
Bloom is generally designed to import your codebase from your upstream repository, massage it to produce a git-buildpakage(GBP) repository for each version of Ubuntu you're releasing into, and make that repository available to the build farm.
If you're trying to use git submodules in the GBP repository, don't.
If your upstream repository uses submodules, you'll either have to extend bloom to support submodules, or release the submodules in your project directly.
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