Applications, Output, generalized eltensor, IC helper functions

This MR replaces !5 (closed) and !6 (merged), plus adds some more contributions. It adds a new "applications" directory. This will contain directories for each MEUMAPPS application, similar to the design of PRISMS-PF. For the time being, I think most of our effort will be on a generalized precipitation application (since that's what we need for ExaAM), but in time I expect that we'll add some others. The bare-bones Allen-Cahn test case is added as another application.

I've also added the first version of a class to handle output. Nominally it supports .vtk and .bov although the .bov code is not currently functional. The .vtk code works in parallel, but yields output that isn't automatically stitched together in VisIt. This is good enough for now, but eventually we will want a more convenient output format. I also added Doxygen comments for this class because I think it'd be a good idea to use Doxygen for the code documentation (or perhaps Doxygen+Sphinx).

I've made some other changes in terms of generalizing eltensor and adding a new namespace of functions to help specify initial conditions.