After running buildr eclispe
and importing the sub-projects into eclipse by default the .git directory in the parent project will not be recognized, and EGit will not work.
The fix is simple:
1. Select all the sub-projects in eclispe
2. Right click Team->Share->Git
3. Select "Use or create repository in parent folder of project"
4. Finish
Alternatively you can import them directly with Git: Import->Git->Projects from Git
.