Several minor changes to eliminate repeated code and/or fold into AbstractApplication class.
1. Removed backup-dir as option and replaced with output-dir.
2. Backups now placed in output-dir by default.
3. setup_backupDir now setup_directories, sets up backup and output directories, all in AbstractApplication class.
4. Removed output-dir from MAGeT.py and pipeline-dir from MBM, registration_chain and pairwise_nlin, since can now use output-dir.
5. Moved self.reconstructCommand() to AbstractApplication class.
6. In subclasses, removed options=self.options and args=self.args to make code-writing more straightforward for other users down the road.