Use parameters to pass legacy flags to MooseApp derived objects
When setting the flags from main.C we were
missing the case where apps were being
created by the Multiapp system. This
patch simply sets the flags in the params
system to avoid this issue. Overrides are still
possible through the [Problem] block.

closes #4111
Merge pull request #4428 from permcody/multiiapp_legacy

Use parameters to pass legacy flags to MooseApp derived objects