Programmatically importing an existing project into Eclipse

Use org.eclipse.ui.wizards.datatransfer.ImportOperation

Try something like this:

IOverwriteQuery overwriteQuery = new IOverwriteQuery() {
        public String queryOverwrite(String file) { return ALL; }
};

String baseDir = // location of files to import
ImportOperation importOperation = new ImportOperation(project.getFullPath(),
        new File(baseDir), FileSystemStructureProvider.INSTANCE, overwriteQuery);
importOperation.setCreateContainerStructure(false);
importOperation.run(new NullProgressMonitor());

You're probably missing a line with

description.setLocation(new Path("/absolute/path/to/project/folder"));