Strip invalid XML characters
Add a new line to the end of generated scripts
Properly control stdout and stderr from command-line

Allow for output of last X lines
Changes back-end implementation of BufferedReaderThread which should
improve performance when stdout/stderr is not retained
Merge pull request #225 from SeqWare/feature/seqware-1893_special_characters_in_stderr_stdout

Feature/seqware 1893 special characters in stderr stdout