Use ApplicationTransactions when indexing commit/audit comments

Summary:
Ref T4896. Depends on D10056. Moves search indexing to standard infrastructure.

Also, fixes a bug where inline comments would not be indexed.

Test Plan: Used bin/search index ... --trace to view index construction of a commit, saw all the comments and inlines get indexed.

Reviewers: btrahan, joshuaspence

Reviewed By: joshuaspence

Subscribers: epriestley

Maniphest Tasks: T4896

Differential Revision: https://secure.phabricator.com/D10057