except for the the exported pdf and ad removal and git you've basically described Pinboard.in I'm pretty sure it searches the content not just the title, tags, and comment you left. It saves a copy of the page so that the site disappearing doesn't mean you've lost the info. It's not downloadable but i don't know why i'd want to backup their backup anyway. It suggests tags / keywords (probably by harvesting the plethora of other people bookmarking things) .

and it's got an API so you could make a command line client.