Does a contractor's written Procurement Manual take legal precedence over its signed Prime Contract (with the Government)?
Unless the agency has a separate clause that is listed in the contract (such as Section H), FAR 52.215-8 - Order of Precedence (Oct 1997), states that the order of precedence is:
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a. The Schedule (excluding specification)
b. Represengtations and other instructions
c. Contract Clauses
d. Other documents, exhibits, and attachments
e. The specifications
Therefore, for the contractor's procurement manual to have a greater precedence than the specification listed in the contract, the contractor would have to include, or make reference to, its procurement manual as part of its representations. It not, then contract clauses, other documents-exhibts and attachments, and the specification would take precedence. (As a side note FAR 52.212-4(s) is the clause for the acquisition of commercial items, but the impression was that the AAP question was relating to no-commercial acquisition).