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The profiling and killing of black men by police is most certainly a civil rights issue.

The NYC division of the ACLU has done work on the illegal and racist stop and frisk law that was in place here, for example.

Not exactly. THe ACLU actually does work in the area being discussed [0]. I believe the criticism is that people did not donate for that reason, not that the ACLU doesn't do anything about it; the ACLU does quite a bit.

[0] https://www.aclu.org/issues/racial-justice

They'd sue the police department. The ACLU sues police departments for violations of civil rights constantly.