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Fixed MPI_Gather* api with sequential write

Various fixes

Fixes for gcc and intel compilers.
gcc-4.1 clean with -Wall -Wextra
intel 11.1 clean with -Wcheck -w1
msvc2010 gives one unrelated warning

Huge update involving update of underlying data representation and
elements management. Different interaction with iterators. New
ElementSet representation.  Some annotation for documentation is added.
New data structures. Examples require update. (check
examples/CMakeLists.txt)

Fix crush - not properly freeing communicators.

some changes