WIP new 'update' command to update and synchronise project metadata

[pjbriggs]

Address issue #893 by implementing a new auto_process.py update command to perform the following additional operations:

• Update relevant paths in the parameter file (when analysis directory has been moved or copied)
• For each project:
  • updates the metadata where it differs from that stored in projects.info
  • updates the list of samples and the paired end flag based on the Fastqs present
  • updates the Fastq directory path stored in the qc.info metadata file in each QC directory
• Updates the list of samples in the project.info file to match the contents of each projects
• Regenerates QC reports when project metadata file is newer than the existing report

In addition there are also updates to ordering of sample names (which should now be more human-friendly).