Replaced DBRef section with references to BSON class table footnotes. Re-ordered sections in order of importance (group helper is least relevant). Removes RST syntax for save flowchart image, which did not appear to work properly and also isn't necessary.

This also re-orders the section to appear before the Collection API changes.

PHPLIB-482: Add missing error expectation to crud tests

The operation field isn't used for anything in our documentation. This was introduced in d5c501a2 and it looks like we missed cleaning it up in later commits that changed every other operation field to null.

The isMaster failpoint can't be reliably disabled again in these tests, causing subsequent test failures.

ChangeStream::getResumeToken() did not exist at the time this test was written; however, we do this assertion in testStartAfterOption().