Braid group actions on branched coverings and full exceptional sequences

We relate full exceptional sequences in Fukaya categories of surfaces or equivalently in derived categories of graded gentle algebras to branched coverings over the disk, building on a previous classification result of the first and third author. This allows us to apply tools from the theory of branched coverings such as Birman--Hilden theory and Hurwitz systems to study the natural braid group action on exceptional sequences. As an application, counterexamples are given to a conjecture of Bondal--Polishchuk on the transitivity of the braid group action on full exceptional sequences in a triangulated category.