This is a bit hard for me to explain, but I’ll do my best:
“Shift + A” marks the whole feed as read. But when having a search query, within a feed, and then using “Shift + A”, the whole feed is still marked as read and not just the items containing the search term(s)
I think this is a bug, because it would make a whole lot more sense to be able to search for a specific term you don’t like and then marking them all as read.
I don’t use the focus aspect of newsblur and therefore would like to manually filter search terms myself.
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I think search is case insensitive. I don’t think you need to worry about using capitol letters in there. True that if you are focused on the search box it shouldn’t trigger the mark all as read function but as a work around, you don’t need to use caps in there anyway.
Sorry, but I think you are missing my point.
The problem I am having is that marking all as read with “shift + A”, marks the whole feed as read, even when I have a search going on.
Yep. I got it 
That is an unfortunate feature. Shift-A is intended to always mark the whole feed as read, not the posts currently showing in the list. I definitely wish it were the latter, though.
The “mark only visible” mark read feature is on my priority list, but not as high as I’d like. I agree, it would be nice to shift+a a search term, but that is a bit of a corner case.
Alright, glad to hear that it’s under your radar.
After seeing Samuel’s comment I realized I didn’t got it. oops.