CORE-5832 Removed obsolete metadactyl.beans namespace.
CORE-6293 Fix for POST /apps and /apps/:id/ui endpoints.

Fix for app validation with tools that have null version, description, or attribution fields.
CORE-6292 Fix for flag params in POST /analyses endpoint.

Fixed metadactyl.analyses.params/flag-args so that it doesn't attempt to trim nil values.
CORE-6190 Validate blank, implicit output filenames.
CORE-6302 Fixed tools in POST /analyses response.

Removed nil values of tool JSON in step components before returning response, since some tools don't have descriptions and compojure-api will throw a validation error, even though the job successfully submitted.
CORE-6301 Fix for PUT /admin/reference-genomes endpoint.

metadactyl.metadata.reference-genomes/replace-reference-genomes calls list-reference-genomes without any arguments.
CORE-6304 Fixed POST /analyses "retain inputs".
CORE-6280 Fixed POST /analyses for stdout/err redirection.
CORE-6306 Fix for saving output parameter 'retain' flags.
CORE-6314: do not attempt to update the batch status when jobs are not part of a batch
CORE-6315: added some database indexes to speed up the analysis listing service
bumped the version numbers
Increased info in missing UUID log msg
CORE-6312 scaffolding for info-typer AMQP service
CORE-5525: removed some dead code from the notification agent
CORE-5525: removed entity field definitions from notification entities, and made a few more changes to clean up the notification agent and facilitate testing