Modernise autotools and fix some platform specific stuff

Modernise autoconf
Modernise automake
Properly quote to avoid AC_LANG_SOURCE error
Change version.h to work on platforms which don't have echo -n
Merge pull request #81 from mp15/autotools

Modernise autotools and fix some platform specific stuff
Merge pull request #82 from srl147/devel

Capture aligner exits in wrapper script.
Move exit check outside function (reading calibration table).
Merge pull request #9 from wtsi-npg/devel

merge changes from wtsi-npg