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Well, first off it was Thomas Ewing, not Ulysses S. Grant that issued General Order #11. Second it doesn't mention any group, race, ethnicity, or religious affiliation - especially not Jewish people. And just to avoid a "he says - she says" here is the order:

General Order № 11.

Headquarters District of the Border,
Kansas City, August 25, 1863.

1. All persons living in Jackson, Cass, and Bates
counties, Missouri, and in that part of Vernon included in this district, except those living within one mile of the limits of Independence, Hickman's Mills, Pleasant Hill, and Harrisonville, and except those in that part of Kaw Township, Jackson County, north of Brush Creek and west of Big Blue, are hereby ordered to remove from their present places of residence within fifteen days from the date hereof.

Those who within that time establish their loyalty to the satisfaction of the commanding officer of the military station near their present place of residence will receive from him a certificate stating the fact of their loyalty, and the names of the witnesses by whom it can be shown. All who receive such certificates will be permitted to remove to any military station in this district, or to any part of the State of Kansas, except the counties of the eastern border of the State. All others shall remove out of the district. Officers commanding companies and detachments serving in the counties named will see that this paragraph is promptly obeyed.

2. All grain and hay in the field or under shelter, in the district from which inhabitants are required to remove, within reach of military stations after the 9th day of September next, will be taken to such stations and turned over to the proper officers there and report of the amount so turned over made to district headquarters, specifying the names of all loyal owners and amount of such product taken from them. All grain and hay found in such district after the 9th day of September next, not convenient to such stations, will be destroyed.

3. The provisions of General Order No. 10 from these headquarters will be at once vigorously executed by officers commanding in the parts of the district and at the station not subject to the operations of paragraph 1 of this order, and especially the towns of Independence, Westport and Kansas City.

4. Paragraph 3, General Order No. 10 is revoked as to all who have borne arms against the Government in the district since the 20th day of August, 1863.

By order of Brigadier General Ewing.
H. Hannahs, Adjt.-Gen'l.

Stupid? Sure. Counter-productive? Most certainly. Racist/antisemitic? Not in the least.