We are using JDev.126.96.36.199.0 and Jheadstart 188.8.131.52.28 with subversion 184.108.40.206.38.60.81. Several JHeadstart files are not appearing in the 'candidates' folder so they are not being placed into the repository. We noticed this when we checked out the application, we were getting errors when running the project because some files were missing. Some of these files are JhsPageTemplate.jsf and jhsRegionTemplate.vm. I happened to keep a copy of the application that went into subversion and these files were not in the candidates folder, yet JDeveloper showed they were not versioned.
I had refreshed the candidates folder a couple of times but it wasn't until I opened up a different application in JDeveloper then went back to my original application and refreshed the folder that the files then appeared.