You might want to have a look at the latest SNAPSHOT.
There are now 4 properties you can set on the configuration to select directories:
def defaultScoobiDir = dirPath("/tmp/scoobi-"+sys.props.get("
user.name").getOrElse("user"))
lazy val scoobiDir = configuration.getOrSet("scoobi.dir", defaultScoobiDir)
lazy val workingDir = configuration.getOrSet("scoobi.workingdir", dirPath(scoobiDir + jobId))
lazy val tempDirName = configuration.getOrSet("scoobi.tempdirname", dirPath("tmp-out-"+hadoopConfiguration.get(JOB_STEP)+"/"))
lazy val temporaryDir = configuration.getOrSet("scoobi.tempdir", workingDir+tempDirName)
This means that if you define the "scoobi.tempdir" property you should be able to direct output files wherever you need. *However* this needs to be done at the beginning of the ScoobiApp before those lazy val get initialised. Otherwise they will be initialised with default values which might be what you are observing now.
Eric.