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Actually, I hadn't. It's possible we could you use it, but's there's a couple of design aspects where it doesn't fit as well:-
we need to make sure that everything works on all shells, not just bash (bpkg is bash only);
it seems to install packages which are more about executables, then functions
It may be that we can actually exploit gitmodules syntax in any event; newer git versions allow out-of tree submodules - so putting a .gitmodules into a module with its dependencies might work (newer git versions also track branches amongst submodules, making this more useful). Given that module installation is only for development, we only need a simple solution. An alternative would just be our own text file and a script wrapping git...
I haven't looked into this project too much, but for dependencies between all the shell modules... have you seen: http://www.bpkg.io/?
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