Merge branch 'release-1.5.4'
Merge branch 'release-1.5.5'
Merge branch 'release-1.5.6'
Prevent Genome Studio Control Probe Profile files being mistaken for
annotation files.

Simplified file format guessing.
Merge pull request #257 from keithj/devel

Improvements to gene expression publication
Improved the reliability with which Sequenom data are found for
publishing to iRODS. This method works around the problem that the
LIMS does not update its plate timestamp when a plate is finished.
Merge pull request #258 from keithj/devel

Improved the reliability with which new Sequenom data are found
Merge pull request #259 from iainrb/devel

Validation functionality for infinium file upload
Updated manifest
Merge branch 'release-1.5.7'
Use iput -k to refresh the checksum
Added a --force command line flag to allow published data to be re-sent
Updated the online help
Added support for capturing the donor_id from the warehouse and adding
it as sample_donor_id metadata in iRODS
Merge pull request #260 from iainrb/devel

Make intensity and MAF/HET metrics optional in collation
Merge pull request #261 from keithj/devel

Added support for capturing the donor_id from the warehouse
Added an Infinium database query to find finished samples by date.

Modified the query which finds samples in a project, plus their data
files, to distinguish re-scans by their date and eliminate duplicate
records being handed to the analysis pipeline. (The pipeline rejects
them.)

Refactored the Infinium database queries to remove some duplication.
The response check was too strict; valid responses are a HashRef or an
ArrayRef, in the event of listing a collection.
Refactored --force flag handling to add elimination of duplicate plate
names.
Ensure that the resultset count is set to 0 in the event of no data.

Also some formatting noise.