You can always create a new Eclipse workspace. The Eclipse.exe -clean
option is not sufficient in some cases, for example, if the local history becomes a problem.
Edit:
Eclipse is mostly a collection of third party plugins. And each of those plugins can add some extra useful, useless or problematic information to the central Eclipse workspace meta-data folder.
The problem is that not every plugin participates during the user-issued cleanup routine. Therefore, I'd say that it is a problem in the system design of Eclipse, that it allows plugins to misbehave like this.
And therefore, I'd recommend to make yourself comfortable with the idea of using multiple workspaces and linking-in external project entities into each workspace. Because, this is the only workaround for the given system design, to handle faulty plugins that spam your workspace.