Still more KernelManager cleanup

Finish up some more work from #2775

closes #2722

- [x] ip/transport configurables only live on KernelManager objects, not ConsoleApp
- [x] fix default ipc paths in `ipython kernel` and `ipython notebook` cases
- [x] fix ipc file cleanup in a few more cases
- [x] add `--transport` alias for all appropriate entry points