Made depth limits of file directory traversal functions optional

Bugfix to use of stat function where returned mtime could be undef
Added new chip design HumanOmniExpressExome-8v1-2
Merge remote branch 'wtsi-npg/devel' into devel
Merge remote branch 'wtsi-npg/devel' into devel
Added David's filter patch to update_infinium_metadata.pl

Changed use hyphen-separated CLI args

Changed log level of counter from DEBUG to INFO
Removed redundant JSON package import
Added a new type of metadata for RT ticket numbers
Added a find_study_title method

Corrected a typo in SQL which was hotfixed, but not committed
Gave dcterms:identifier' an exported metadata key
$INFINIUM_SAMPLE_NAME

Refactored publish_analysis_directory to use $INFINIUM_SAMPLE_NAME to
cross-reference samples to the analysis (it's primary metadata) and
to be more efficient in iRODS lookups.
Added replacements for publish_sample_data.pl. These split the
file-finding from the publication step.
Changed log4perl setup to log user activity to daily log files
Updated test for known SNP sets
Upgraded some debug log messages to info level
Added the option to fork processes to update chunks of objects in
parallel
Added support for the 'like' operator in imeta queries
Uncommented one line comitted in error

Fixed a log message typo
Minor changes to a log message and perldoc
Resolves RT #351930 by adding new columns to the microarray loading
manifest and using the plate and well information therein to find
samples in Sequencescape
Added info-level progress log
Added expression manifest test