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Every document released under FOIA is hand reviewed, unless the document was publicly available anyways. For example, you can get a large number of "The Army's guide to X" and similar documents either from military's website.

In the case of government contractors, the appropriate government agency issues a letter to the contractor. The contractor has the chance to censor almost anything if they consider it a trade secret. There are other reasons for censoring, but the government themselves generally makes those decisions. Contractor's are completely OK with this because they get paid hourly to do the work.