Fix for --disable-xdr
-Wshadow warning fix
Don't pollute other code with local macro definitions
Updating Neveln, 2014.
Adding Prudencio preprint.
Adding 'partition_agnostic' argument to equation systems read and write to be able to turn off renumbering
Merge pull request #189 from friedmud/disable_renumber_pr

Allow disabling renumbering for equation systems read / write
specify serial tests when using newer automakes
dervied files from bootstrap
update gcc coverage
cast to a std::size_t rather than assume, fixes cygwin
include Hilbert/Algorithm.hpp to resolve linking on cygwin
include <cstdio> for FILE definition
Derek's build script
Python build script