As suggested by @roystgnr, creating a new UniquePtr type to allow
usage of the old AutoPtr type to be deprecated gracefully.

Use a global variable to ensure only one deprecated warning from
AutoPtr and not one per template instantiation.
AutoPtr -> UniquePtr in library and examples.

We may be able to use configure tricks to default the new UniquePtr
type to the old type until we are officially ready to switch
everything over.
Reindenting headers and src after AutoPtr -> UniquePtr update.
Adding AC_ARG_ENABLE test for --enable-unique-ptr
Ran bootstrap.
Use libMesh's AutoPtr as the UniquePtr when configured with --disable-unique-ptr.