I think you meant to have Pi instead of ? on the second set of code.
Manipulate[
Module[{t, cols, rotproj1, rotproj2},
t = 1/2 - (-1)^Floor[s] Cos[Pi s]/2 + Floor[s];
cols = RGBColor /@ {"#D8FFF1", "#5B73A7"};
rotproj1 =
RotationMatrix[
Pi/2 - ArcTan[
Sqrt[3/5]]].({{Cos[Pi], 0, 0, -Sin[Pi]}, {0, 0, 1, 0}} /.
Pi -> Pi/
2 + .0001).permutohedronProjectionMatrix[5];
rotproj2 = ({{Cos[Pi], 0, 0, -Sin[Pi]}, {0, 1, 0, 0}} /. Pi -> Pi/
2 - .0001).permutohedronProjectionMatrix[5];
Graphics[{Thickness[.01], cols[[1]], CapForm["Round"],
JoinForm["Round"],
Line /@ ((1 - Min[t, 1]) (rotproj1.# & /@ # & /@
permutohedronEdges[5]) + (1 -
Abs[t - 1]) (rotproj2.# & /@ # & /@
permutohedronEdges[5]) + (Max[t, 1] -
1) ({#[[1]], -#[[2]]} & /@ # & /@ (rotproj1.# & /@ # & /@
permutohedronEdges[5])))}, PlotRange -> 5,
ImageSize -> 540, Background -> cols[[2]]]], {s, 0, 2}]
But other than that, pretty cool!