We\'ve got a multi-module project using Eclipse and Maven. The only way I could get it to work in the past was to use a flat layout for the projects, where the parent module was
Is it possible that you are working with old versions of the tool?
I have a Maven multi-module project that I work with using Eclipse 3.7 (Indigo), M2Eclipse (1.0) and EGit (1.0).
On the file system the multi-module project has a single parent directory.
In Eclipse I have separate projects for each module.
M2Eclipse does the dependency management perfectly.
There is single git repository (.git directory) at the top-level and EGit works perfectly.