PHPLIB-438: Unify handling for write stages in aggregation pipelines

[alcaeus]

https://jira.mongodb.org/browse/PHPLIB-438

[jmikola]

Some documentation changes are needed here (both RST and maybe Aggregate's doc blocks). We have quite a few references to $out where we reference it as the only write operator.

Based on https://docs.mongodb.com/master/reference/method/db.collection.aggregate/, the manual started referring to "$out and $merge stages", so we can probably do the same.

[alcaeus]

Review items applied, documentation updated. I also added read and write concerns to the Context::fromCrud helper to fix intermittent test failures on replica sets.

[jmikola]

Question about Context::fromCrud(), but feel free to leave as-is if it's truly needed. Folks in #driver-devs may be able to confirm whether those options should be necessary.

[jmikola]

Was this (and outcomeFindOptions) actually needed? AFAIK, all of the CRUD tests read/write to the primary and never specified a custom read concern or read preference.

AFAIK, defaultWriteOptions was only used for transaction tests (per implementation instructions).

[alcaeus]

I added this after a test kept failing on a replicaset setup. I got suspicious after I couldn’t replicate the failures when step-debugging through the test and thought that the problem might be with the secondaries being read before they have the data.