Version 0.55, April 2013

1. Bug fix.  Pipeline arguments included in an instance were not added
to the pipeline arguments.

2. Ensured that all files listed as intermediate files were not included in
the '.all' section.  As it stood, files still appeared as an output despite
being an intermediate file.  This meant that rerunning a makefile would
regenerate files that were not required.

3. Added the pipeline build-moblist-align.  Cats together reference fasta files
and then aligns to this reference.  Pipeline includes an internal loop.