Ensure index is used when running on MySQL

[jonnystoten]

This PR fixes a performance issue when running notary server with MySQL. When calling GetCurrent to find the most recent metadata file for a GUN and role, we use this snippet:

q := db.Select("updated_at, data").Where(
	&TUFFile{Gun: gun.String(), Role: tufRole.String()}).Order("version desc").Limit(1).First(&row)

First adds an additional order by clause for the id column, so this corresponds to SQL roughly like:

SELECT updated_at, data FROM tuf_files WHERE gun = ? AND role = ? ORDER BY version DESC, id ASC LIMIT 1

We have an index on gun, role, version, and adding the order by on id prevents this index from being used. Usually adding the primary key should be OK but because it's being added in the opposite direction (version is DESC and id is ASC) it doesn't work. We don't need to add this primary key sort because gun, role, version already uniquely identifies the row.

In the latest version of gorm 1.x there is a new method Take which behaves in the same way as First but doesn't add the primary key sort. From some quick testing on Docker's notary instance, removing this from the query reduces the time this query takes on a very large repository from over 30 seconds to a few milliseconds.

The main fix here is using Take instead of First on the GetCurrent method. I've updated all usages of First to Take in that file for consistency - I don't expect them to have much impact on performance. All of the other changes were necessary because of the gorm upgrade.