add option to embedFonts shell script
Fix concatenation fn

* Sort rows of output matrix by name.
  Also affects taxon list if that option is used, making it much
  easier to see whether taxa contain typos in some input matrices.
* If no output file given, return the nexus file, rather than
  printing it out.
fix output of concatenation fn

* writes to stdout if no output file is given
* returns nexus as R object for interactive use
* more robust input checks for shell script
* messages use `message()` instead of `cat()`