CORE-4002: Added docs about replacing reference genomes

Added a line that says that reference genomes are completely replaced by the import endpoint.
CORE-4802: allow arbitrary status transitions for tool requests
CORE-4802: allow new service codes to be added
CORE-4802: updated the tool request service documentation
CORE-4802: added an endpoint to list tool request status codes
CORE-4802: added tool the tool request status code listing service to the endpoint index and to the table of contents in the tool request services file
CORE-4350: bumped the metadactyl dependency version
CORE-4350: implemented the guts of the Clojure version of the permanently-delete-workflow service
CORE-4350: updated the documentation of the permanently-delete-workflow service to indicate that it no longer support deleting analyses by name
CORE-4350: added some validation to the permanently-delete-workflow service that was present in the previous implementation
CORE-4350: reimplemented the delete-workflow service in Clojure
CORE-4350: removed the AnalysisDeletionService import
CORE-4350: removed an extraneous space
CORE-4350: added some documentation to indicate that an attempt to logically delete an app that has already been marked as deleted is not treated as an error condition
CORE-5132: decode the "search" query parameter in the search-analyses endpoint before performing the search
Merge branch 'dev'

Conflicts:
	project.clj
bumped the version number
Merge branch 'dev'

Conflicts:
	project.clj