Peter Jurgec (faculty) and Bronwyn Bjorkman (former postdoc, now at Queen's University) have a paper now published in Phonology, 35(4): "Indexation to stems and words."
This paper presents an extension of indexed constraints, such that they can apply not only to individual morphemes, but also to potentially complex constituents such as the stem. This modification allows us to capture a class of long-distance morphologically derived environment effects (MDEEs) that have been previously unexplained. MDEEs typically involve an exceptional phonological pattern that is lost under affixation. Formally, MDEEs are predicted if complex constituents such as stems are treated as lexically exceptional only when every morpheme contained within them is independently exceptional. This approach further predicts asymmetries between bare roots and affixed words, between roots and affixes, and between inflected and derived words. All other things being equal, the first of each pair is more likely to be exceptional in more contexts.