"Exclude content..." not excluding...anything

Background: I decided long ago that I wanted a single Flare project as a full content repository, and that I'd use TOCs to drive what content should be in outputs. And I thought I'd gotten this resolved before, but in my most recent HTML5 builds, it looks like the output contains pretty much every file in the project, topics, images, everything.
I remember seeing this discussed before--I think I was even a part of at least one of those discussions--but I can't find any. (Interestingly, search the forums here for the literal text of the setting, "Exclude content not linked directly or indirectly from the target," and the forum search returns no results.)
I'm not sure where to even begin to start searching to track down the root cause.
This is an issue because the product-specific help systems return search results that include topics that are not for that product. This just cannot happen.
I remember seeing this discussed before--I think I was even a part of at least one of those discussions--but I can't find any. (Interestingly, search the forums here for the literal text of the setting, "Exclude content not linked directly or indirectly from the target," and the forum search returns no results.)
I'm not sure where to even begin to start searching to track down the root cause.
This is an issue because the product-specific help systems return search results that include topics that are not for that product. This just cannot happen.