Changed vector input to RAtoAi to a reference input, added alternative formulation but commented it out

significant speedup
Changed vector inputs into reference inputs in all places possible
Merge branch 'Ben's-Branch'
Added matrix powers kernel, slow but it works

Also figured out how to link files recursively to each other
Merge branch 'Ben's-Branch'
Fixed stupid leftover error
Merge branch 'Ben's-Branch'
Merge branch 'master' into Kyle's-Branch