Fixing indentation in headers after recent round of tab removal.

The problem seems to be that Emacs opens headers in "C mode"
rather than "C++ mode" and thus was not reindenting them properly.
Fixing indentation in source files for consistency with headers.
Running reindentation script on example source and header files.
Running reindentation script on test source and header files.
Adding reindent.sh script which can reindent entire files according to
the libmesh coding style.

May eventually become part of the 'make beautify' target.
Merge branch 'reindent_files'