Use `vdot` vs `inner` vs `dot` consistently in the source

[pnkraemer]

They all have slightly different behaviour (eg regarding flattening and conjugation), and currently, matfree uses all of them for the same tasks (typically, inner products of two vectors), which I find a bit confusing. I think we should recommend all but one and use that consistently.

Relatively low prio, since purely internal and unrelated to functionality.