Reworked array input, changes in intersectCollect master template, changed some flagnames, enabled target file autovivication

- Added “!” to regexp for clarity (merge and rank).
- Fixed order of file template generation in rank module
- Reworked how input arrays are handled by MIP
- Added “s” to target file —flags
- Enabled target files as comma seperated list on cmd
- Enabled autovivication of target files when non-existent
- Enabled default of target files when parameter not supplied
- Updated the annular module for ANNOVARs latest changes (vcf4old, maf_threshold reserved for 1000G)
- Removed -numBad flag for GATKVariantRecalibrator version 2.8-1