Remove Options::isSet()

Replace uses with alternative means.  Add storeIsSet() to all options to
make it convenient to just check whether an option is set.
Remove Options parameters from methods where its only purpose was to
provide access to isSet(), reducing exposure of the concrete class and
making the interface cleaner.

Change-Id: If1207c8cf3af86e306c52748f8878480e35e2fc0