Is it true that you cannot add non-commercial clauses to a commerical contract? What alternatives do we have to address this situation where we have a commercial service, but a non-commerical product and we want the data rights to the non-commerical end product?
It is true. FAR 12.301(a) states:
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(a) In accordance with Section 8002 of Public Law 103-355 (41 U.S.C.264, note), contracts for the acquisition of commercial items shall, to the maximum extent practicable, include only those clauses --
(1) Required to implement provisions of law or executive orders applicable to the acquisition of commercial items; or
(2) Determined to be consistent with customary commercial practice.
Regarding the data rights issue, FAR 12.211 states:
...the Government shall acquire only the technical data and the rights in that data customarily provided to the public with a commercial item or process.
Those two references taken together indicate that if you truly have a commercial contract employing FAR Part 12 procedures, then a non-commercial data rights clause should not be used. This prevents possible abuse of Congress' original intent when it passed FASA in 1994. However, is this a valid commercial contract? A case could be made that because the end item is a non-commercial item, then FAR Part 12 may not have to be used in this case. That's something for the contracting officer to consider.