refactor(format): make formatting explicit instead of bus-driven

Replace the implicit Bus.subscribe(File.Event.Edited) formatter with
an explicit Format.run(filepath) call in write/edit/apply_patch tools.

This ensures formatting completes before FileTime stamps and LSP
diagnostics run, rather than relying on the bus to block on subscribers.

- Add Format.run() to the Effect service interface and legacy adapter
- Call Format.run() in write, edit, and apply_patch tools after writes
- Remove Bus subscription from Format layer