I am using Spring Tool Suite(STS) 3.0.0 release (eclipse.buildId=3.0.0.201208091018-RELEASE-e42). It was running fine for a couple of months but lately my main workspace is
I had the same problem after opening a Kepler workspace with Luna and then switch back to Kepler. Seems that Luna added some data unexpected by Kepler.
I had to remove the .metadata folder and configure the workspace again.