If you ever wanted to copy the full workspace to another machine you may have noticed that a billion generated files (e.g. bin) are copied and that this takes a long time. If you start Eclipse with the -clean option the workspace will regenerate all file again.
You can avoid this bye de-selecting in the “Build automatically” in the preferences under General -> Workspace.
If you now select Project -> Clean -> All and de-select “Start an Build automatically” in the dialog you end up with a workspace without the files of the build process.