Updated applications to explicitly use self.outputDir, which is set in AbstractApplication, prior to when run() is called.
* Modified _setup_directories() to include underscore at beginning of name. Function now explicitly called, rather than called in _setup_pipeline()
* self.outputDir now explicitly used in: LSQ12.py, LSQ6.py, MBM.py, NLIN.py, twolevel_model_building.py
* removed setup_backupDir function from MBM.py that was never used. (Likely from earlier iteration)