I was able to upgrade an existing workspace from Luna to Mars and was without issue for a couple weeks.

A coworker then setup a new laptop and was unable to get the project to import correct. The build path is setup as "src" not "src/main/java" as would be expected. Project is a Java EE7 war app.

I then deleted the project on my working mars and ran into the same issue on import. This is with a full delete within eclipse (including on disk) and a fresh clone from github.