CORE-4017 Updates for setting App integration_date.

App published date is now only set when it's initially made public, unless an 'updateVetted' flag is set.
CORE-5351: added a missing parameter
CORE-5340: modified the internal to external app JSON translation code to work with the new values of reference genome parameters
CORE-4979: fixed an incorrect function call
CORE-5123: added command-line options to allow the user to override the locations of the database initialization files
Updated buckets endpoint documentation
CORE-5168
CORE-5356: updated the permissions model used by the coge file ingestion code when sharing files with the coge user
CORE-5157 modified queries to consider only distinct

The data object count query was modified to only count distinct data Ids.

The data objects listing query has been made a little more complicated. For each set of entries with the same Id, it selects only the one with the lowest replica number.
Merge branch 'dev' of https://github.com/iPlantCollaborativeOpenSource/DiscoveryEnvironmentBackend into dev
CORE-5361: accept either sortField and sortDir or sortfield and sortdir as app listing parameters
CORE-5358: added a column for email templates to the tool_request_status_codes table
CORE-5358: modified donkey and iplant-email to allow email messages to be sent for arbitrary tool request status codes
CORE-5353 Fixed error reporting in /secured/(un)share endpoint.
CORE-5353 Fixed desired perm check in shared? function.

Fixed logic by checking desired permission keyword against a current permission keyword, rather than checking against a permission map.
Bumped version to 3.0.2.
Finished bumping kifshare version to 3.0.2
Bumped metadactyl's version to 3.0.2.
CORE-5368: Fixed a typo in the permissions.clj file.

We were calling set-permissions instead of the set-permission.
CORE-5368: Fixed a funky donkey (cond) that was failing on first login.

We weren't first checking for the directory's existence, so the call was
failing when validations were fired.
Merge branch 'dev'