Added fix to gnuplot code in order to make sure it compiles properly on Mac.

Added .in files (generated by autotools), to ensure people can do a quick install after cloning the git repo.
Fixed an overflow bug with SECT, where sequences of over 64K in length, we not handled correctly.

Added and fixed unit tests.  Unit tests can now be run by typing "make check" assuming the boost unit test framework is installed.
Merge branch 'GITHUB/master'  This incorperated markdown version of README made by Jan van Haarst.

Also updated README to provide details of how to clone the git repo via ssh and https.

Modified Makefile.am to accept the new markdown README.