configurable newline string when writing alignment and other flat files

Jalview version 2.6.x and prior use hardwired newline character codes ("\n") in many of the file output routines. This is not strictly platform independent (see this article: http://www.stevengould.org/portfolio/SunWorld/swol-11-1998/swol-11-javaapps.html), since best practice is to write lines using the local newline format (as generated by system.out.println does).

It may also be important to be able to control the newline character used when a specific platform is targeted - i.e. form textarea content is normally encoded with \r\n line separators.