Dialyxir will now (as of latest release) invoke the dialyzer --check_plt task which should handle updating apps modules when dependencies have had code changes. It is correct it does not remove apps, this is a liability of the global PLT and should definitely be fixed when I move to the dialyze style PLT management.
dialyxir gets transitive dependencies using Mix.Project.deps_paths - basically the same contents as the mix.lock file. I am not pulling in OTP applications from dependencies applications list and perhaps I should - is that what you see is missing?
