> It's a search box that many people will use exclusively to search for _local_ content.
That still doesn't make it a privacy violation, since you know where your searches are going (as does any other user, since it's obvious based on the results).
> Why should Amazon know what programs and files I'm using?
It makes the normal user's life more convenient since he doesn't need to figure out which box to type something in. You think that's ridiculous? Users are well known for typing web addresses into any box available. They cannot tell the difference. Having a single box for everything makes for a better experience,.
Amazon doesn't know what programs and files you're using, since Canonical anonymizes it. If you don't like it, or you don't trust Canonical, and you still want to use the "search everything" search box, then adjust the settings to do what you want.