Let Y be a closed and oriented 3-manifold. We define different versions of unfolded Seiberg-Witten Floer spectra for Y. These invariants generalize Manolescu's Seiberg-Witten Floer spectrum for rational homology 3-spheres. We also compute some examples when Y is a Seifert space.

We use the construction of unfolded Seiberg-Witten Floer spectra of general 3-manifolds defined in our previous paper to extend the notion of relative Bauer-Furuta invariants to general 4-manifolds with boundary. One of the main purposes of this paper is to give a detailed proof of the gluing theorem for the relative invariants.

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Kronheimer-Mrowka recently proved that the Dehn twist along a 3-sphere in the neck of K3#K3 is not smoothly isotopic to the identity. This provides a new example of self-diffeomorphisms on 4-manifolds that are isotopic to the identity in the topological category but not smoothly so. (The first such examples were given by Ruberman.) In this paper, we use the Pin(2)-equivariant Bauer-Furuta invariant to show that this Dehn twist is not smoothly isotopic to the identity even after a single stabilization (connected summing with the identity map on S2×S2). This gives the first example of exotic phenomena on simply connected smooth 4-manifolds that do not disappear after a single stabilization.