API: Organize classes

* Group methods in ApiBase by function
* ApiBase::validateLimit and ApiBase::validateTimestamp are now
  protected; there are no callers in any extensions in Gerrit
* Group methods in ApiQueryBase by function
* Move ApiFormatFeedWrapper out of ApiFormatBase.php
* Deprecate some methods in ApiQueryBase that seem useless and are
  unused in core or any extensions in Gerrit

Change-Id: I32092f13906b6826d2137401724c21ccefa6f670
Merge "API: Organize classes"