[FileCheck] Report missing prefixes when more than one is provided.

If more than a prefix is provided - e.g. --check-prefixes=CHECK,FOO - we
don't report if (say) FOO is never used. This may lead to a gap in our
test coverage.

This patch introduces a new option, --allow-unused-prefixes. It
currently is set to true, keeping today's behavior. After we explicitly
set it in tests where this behavior was actually intentional, we will
switch it to false by default.

Differential Revision: https://reviews.llvm.org/D90281