Jay's treaty that stated that American merchants would not be discriminated against is a status called most favored nation. It is not the status of quasi war, alien and sedition, or limited trade agreement.
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Being discriminated against for your religion
Early Americans discriminated against "african americans" and "american indians' A: Also the Chinese who worked, not only on the transcontinental railway system, but on many of the railroads in this country.
You have to be more specific as to when, because various groups have been discriminated against at different times. Chinese immigrants were discriminated against on the west coast at one time, as were Catholic immigrants.
Every race has been discriminated against just as every race has discriminated against others.
The American rebels in the American Revolution were fighting for their rights and their country against the mother country, Britain. On the other hand, the Loyalists remained supportive of Britain against the rebels in the war.