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From Michele's review of the IBI/ITC interactions:
Term loan upfront fees should be amortized over the term of the debt (see p. 3 left column publication 551) – the IRS likes this because it spreads out the tax deduction. The only other alternative for income tax purposes is to treat them as expensed at the time they are incurred (COD). It doesn’t look like SAM is including these costs in the costs applied to the manual allocation of costs to different depreciation terms (and additionally, 3% has been excluded from the latter). However, upfront fees are also not flowing through income taxes as they would be if they were treated as expensed at COD. I think the same issue is applicable for the 3% of costs that have been manually excluded from the depreciation basis calcs.
Investigate how SAM should deal with these costs.