Use "git log ... --stdin" instead of "git log ... --not ..." to avoid oversized command lines

Summary:
Depends on D20853. See PHI1474. If the list of "--not" refs is sufficiently long, we may exceed the maximum size of a command.

Use "--stdin" instead, and swap "--not" for the slightly less readable but functionally equivalent "^hash", which has the advantage of actually working with "--stdin".

Test Plan: Ran bin/repository refs ... with nothing to be done, and with something to be done.

Differential Revision: https://secure.phabricator.com/D20854