Remove docs from EXTRA_DIST target

Having docs there would cause Doxygen to be run when `make dist`
is run. However, the docs target was removed from the Doxygen target
list, so this was giving me trouble with make dist(check). We probably
don't want to distribute Doxygen stuff anyway and should get around
to setting up the webpage with Doxygen documentation...
Clean up files generated by one of the new tests

This was causing `make distcheck` to get upset.
Propagate required libraries to make distcheck

By default, nothing will get propagated. In theory, when configure
gets run during make check, it will look for LIBMESH_DIR, BOOST_DIR,
etc. However, sometimes I don't have LIBMESH_DIR set, for example,
so this way we can ensure make distcheck will use the required libraries
that we are currently using. Won't bother putting in the optional ones.
Merge pull request #126 from pbauman/distcheck_fixes

Distcheck fixes