Last C++ release

This is the last Synder release that is written in pure C++. All subsequent releases will be R packages that wrap the current code. Eventually I will write a command line interface to the R package that will be nearly identical to the current one (though not implemented in C++), but for now, if you need a command line tool, you can clone this release. Apart from a serious bug in GFF input parsing (breaks for long 9th column entries), everything should be fine.