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 a peer to the other modules. This worked fine with m2eclipse and Subversion.
Now we'd like to move to Git and GitHub. I'd like to expose the entire project, along with all the modules, as a single project on GitHub. The problem is that EGit, the Eclipse/Git plugin, wants to manage projects one at a time, not groups of projects, and so if you've got a flat layout, you can't do it.
The right answer is to use a standard Maven hierarchical layout and manage the parent and all the modules as a unit. But Eclipse doesn't like that, and no amount of fiddling will get Eclipse to accept nested projects. m2Eclipse does not support hierarchies: https://issues.sonatype.org/browse/MNGECLIPSE-2291
So what do you do? Do Git from the command line and abandon the ability to see what files have changed in Eclipse? Or abandon Eclipse?