Invert include/exclude logic on DivinerAtomQuery

Summary: Fixes T8401. Change withIncludeGhosts() to withExcludeGhosts() and withIncludeUndocumentable() to withExcludeDocumentable(). In particular, this allows querying for atoms by PHID to work as expected.

Test Plan: I got confused with double negatives so I might have gotten some of these wrong... I poked around Diviner and re-generated documentation to verify that this is working as expected.

Reviewers: epriestley, Blessed Reviewers

Reviewed By: epriestley, Blessed Reviewers

Subscribers: Korvin, epriestley

Maniphest Tasks: T8401

Differential Revision: https://secure.phabricator.com/D13157