Oops, one more library AutoPtr fix.
Making examples compile with new AutoPtr implementation.
Updating boost.m4 so libmesh can use unique_ptr.hpp

* Use $top_srcdir instead of $srcdir
* When using libmesh's boost distribution, add it to
  libmesh_contrib_INCLUDES.  This way, it can be used while building
  tests and examples.
* Adding $(libmesh_contrib_INCLUDES) to AM_CPPFLAGS in
  examples/Make.common
Ran bootstrap