Collated Improvements

Switch Trinidad to Puma
	60% reduction in memory requirements when in operation, superior handling of concurrent requests.
Updated support for latest Jruby
	Avoids being tied to old versions of Jruby and the JVM allowing us to take advantage of bug fixes (Including security) and performance improvements
Removed redundant controllers
	Mostly admin only controllers, which were broken anyway. Also a deprecated submission creation page which was still accessible through a convoluted link burried in a sidebar somewhere.
	Also includes removal of the ability to destroy various core resources (such as request types and studies), the former especially would break half of Sequencescape were someone to actually attempt it.
General refactoring and cleanup
Remove unwanted temporary tables to a backup database
Reduced time taken to run test suite by 50%
Improved validation of bulk submission to reduce user errors
Improved error messages returned to user with invalid submission
	- The user no longer sees the complete stack trace
	- The error messages will identify which samples are missing required fields
Updated the JDBC drive
	Performance increase, seems to be ~30% if the test suite is a good judge
Added Reference genome to the API

Fluidigm: wells that end up on the scrathpad will no longer have the samples removed from downstream plates
Users will be once again able to access pacbio worksheets once a batch has been released

Rails now knows that requests can only belong to one batch
	This restriction was previously enforced at the database layer only.