"After all of the talking and posturing and all of the other crap going on what this all hinges on is Muslims are commanded by Allah to exterminate every Jew on the planet. That is at the base of everything that is happening. It doesn't matter if it is Sunni or Shia Muslim they all are commanded to exterminate Jews."
Nope; that's a common misconception encouraged, depended on by people with a political agenda of fear-induction; Quran, Surah 9:5 "And when the forbidden months have passed, kill the idolaters [note: "idolators" is also sometimes translated as "polytheists" -given the period during which the Quran was written, it is reasonable to assume its intended subjects are the Catholic Church, Roman, Egyptian, Levant area polytheists although Hindus can't be ruled out considering the Spice Road was open and active] wherever you find them and take them prisoners, and beleaguer them, and lie in wait for them at every place of ambush. But if they repent and observe Prayer and pay the Zakah, then leave their way free. Surely, Allah is Most Forgiving, Merciful."
The fundamental difference between Islam and Judaism is about the same as the difference between Judaism and Christianity -i.e. minor; they're both monotheistic, aligned with the god of Abraham (YAllahweh so to speak), share Abrahamic tradition minus the circumcision, share most of the 10 Commandments, etc.
Now, if we're talking about fatwahs which have been issued over the last 70 years decreeing war on Israel specifically, Jews generally, that's a different story and yes, of course, that's a thing. But that steers back to impact on Palestinians of the Israeli government's expansionism and the turning of a blind eye, active facilitation, aid in covering up when its own commit extrajudicial killings. Add to that Israel's rumored nuclear capability, it's demonstrated willingness to take land from other nations by force (Golan Heights taken from Syria) and the distinction between who's wearing the white/black hats starts to get hazy.