Many of the BPEL projects create empty folders that don't look like they are used. For example, the "HelloWorld" project contains a "HelloWorld" folder.
Also, the BPEL editor automatically adds the "bpel" namespace prefix to a file if it does not already have this prefix defined. This causes the editor to show as "dirty" the first time it is opened, even though it hasn't been touched (see https://issues.jboss.org/browse/JBIDE-9303). This is a different problem, but for now we should add this prefix to all of the examples, as a quick fix.