Database class parameter and documentation cleanups

Database class parameter and documentation cleanups

* Document various parameter arrays.
* Fix $user = false loophole in Database::__construct().
* Set the Postgres port *before* calling super, as it is
  needed by open().
* Remove 'chronProt' parameter as it is lazy-loaded.

Change-Id: Icc1037efa1eee7ae6fdd2919f60001e6e29ae55c