Stan,
A lot of this is from my memory of Ian Kershaw's book, specifically on how the Holocaust developed to the extent it did out of the German war effort in the East. Timothy Snyder's The Reconstruction of Nations also has a lot of good stuff on Lithuania and Poland, specifically on the development of ethnic nationalism separated out different groups which previously did not define themselves by ethnic categories. Most of the slaughter of the Jews in the Baltics was in Latvia and Lithuania - Estonia had a very small Jewish population, IIRC.
As for the slaughter of Jews in the Baltics, a large number of these were not "national" Jews because the Germans shipped many Jews from all over Eastern Europe to Baltic camps for extermination. Vaivara, for instance, housed thousands of Jews from all over the Baltics in Estonia, and thousands of Czech Jews were shot at Kalevi-Liiva (US HHM website).
Not to take the focus off of German anti-partisan operations to refocus on the Holocaust - my post was meant to introduce the fact that the German conception of anti-partisan operations was inevitably wrapped up with their overall political conceptions at the time.
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