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.
Fixed the version of tools.cli used by heuristomancer.
Modified the config stuff in clojure commons to support reading from a
file.
Modified donkey to add command-line options.

Added a setting for --help, --config, and --port.
Cleaned up iplant-email a little bit.
Modified iplant-email to use command-line settings.
Moved to newer tools.cli and added the --config option.