Apply exclusion/inclusion pattern filters and then execute the requested transformations in canonical order.

The method follows a three-phase approach:

1. Exclusions — rules matching any exclusion pattern are removed.
2. Inclusions — if inclusion patterns are configured, only rules matching at least one pattern are kept.
3. Transformations — each requested transformation is executed in the fixed canonical order, with before/after/error hooks invoked around each execution.

The method uses a readonly string[] internally during the transformation loop to avoid unnecessary array copies; it only materialises a mutable copy at the very end.