SI-5675 Discard duplicate feature warnings at a position

When -feature has not been enabled, we were double counting
identical feature warnings that were emitted at the same position.
Normal error reporting only reports the first time a warning
appears at a position; feature warning counter incrementing
should behave the same way.

@hubertp: Fixed .check files that were broken in the original commit.

Re-submission of #2067.
I was the reviewer of the original PR and apart from the .check files everything LGTM.
So I guess review by @retronym