That's a good question. If you use git sub-tree, then as far as Stash is concerned you have a single repository and everything, including Jenkins, will continue to work fine. Keep in mind that you may end up 'reviewing' the same code multiple time, depending on how/where you import your modules/plugins.
If you were talking about git submodules then I'm afraid the answer would be less satisfactory, as we don't (yet) have cross-repository pull requests. Jenkins/Bamboo shoudl be able to build/clone repositories with submodules though.
Dependency management with Git is an area that I don't think has been solved by anyone satisfactory yet - you might be interested in this recent blog from a colleague of mine.
Best of luck.
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