Remove hardcoding of path to java executable
Fix MANIFEST - legacy file left in generating false warning
remove spuriously merged file

functionality of this "classic" is in bcl2bam_phix_deplex_wtsi_stage1_template
use samtools_cmd as subst id for samtools and remove Sanger specific path to samtools-1.1
Fix template name and description

no need to call stage2 as no treatment of existing PhiX alignment.
Merge branch 'dkj-devel' into devel