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.