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First of all, lots of overlap and unsubstantiated charges there.
I have no problem with the FBI or other departments compiling information about PETA, Greenpeace and other fringe groups that may or have become violent or support terrorists. In fact I'd be upset if those groups were NOT being looked at. The articles don't make it clear that these people were wiretapped, or if they were if it was without a warrant. In some cases all that happened was a dossier was compiled. Good!
Have you ever seen an ANSWER rally? You have people advocationg the overthrow of the government, pledging jihad, supporting our enemies, etc. These people need to be monitored.
Leaking the NSA program was harmful and SHOULD be investigated. If someone in the government leaked it they should be tried for treason and face the consequences.