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Steps to reproduce: 1) clone a git repository with submodules (http://git-scm.com/book/en/Git-Tools-Submodules) 2) In Eclipse import as existing project a project inside a submodule 3) Team -> Share -> Git 4) look for a way of doing so 5) fail There's no way to link the two if the project is within a submodule. I tried with any order of operations (importing directly from submodule in the Git Repositories view) As a side note: I think this is a design mistake, the same design mistake eclipse did with maven: trying to integrate by re-writing the tool in java instead of actually using the tool itself (like you did with ANT for instance) by executing it as an external tool and wrapping the responses.