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The more I think about it the more I think you may be going about this the wrong way. You don't have a project with a number of submodules, you really have a number of separate projects all of which require a submodule containing the core code base.
This is true. The strategy is to extract the core code into a separate submodule so the application can link to whichever version of the core code they want to use. This core stuff has been refactored so it is all under a sub-directory ready to be moved. Once this has been done and everything is settled, the rest of the code base will be split out until everything is separated.
