Stop using package mathtools and therefore \shortintertext

This is to fix overlapping footnotes again. That it works is just a
fluke I guess: the conflicting equation-footnote pairs simply disappear
because the equation is moved elsewhere. But as good as it gets.
Remove unused nomenclature
Remove void spurious equation
Increase footskip to avoid equation overflowing over footer

Allow equations produced with amsmath align to break over pages as well
for good measure