updated merge Script: a list of all copied files is generated. This list is used in the next merge to first remove all the old files before copying new ones.
clarified comments
added code for avoiding the deletion of package.mo and package.order files
Merge pull request #44 from Mathadon/removeOldDirs

Remove old dirs
Merge branch 'master' into issue43_refactor
Removed unused import
Changed name to a hidden file name
Corrected bug that caused reference results not to be added to copiedFiles.txt
Revised file to make copy entries as a relative path