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It is unsurpising that Army spokespeople might want to sow confusion by this blatant misdirection, but as you mention (without profanity - to your credit) there is absolutely NO reason for the press to go along with this. If it were merely laziness, it would be one thing but it's absolutely clear that the only reason for the change in terminology is an after the fact justification for our presence in Iraq and to sway US public opinion toward our continued participation in their civil war.
I suppose in the long run "Al Qaeda" is going to end up like "Kleenex" or "Aspirin". Something that was once a trade-name but has come to such common usage as to be a generic term for the category. That such laziness is being encouraged by the American press remains unforgivable.