Cleaned up tmp / final dir handling; eliminated outPathOrg; issue - cannot handle incremental situation (fastqDump once, then fastqDump again) due to renaming to preexisting dir (the dir renameis essential to atomicity though). 


git-svn-id: svn://svn.r-forge.r-project.org/svnroot/aroma-dots@3582 edb9625f-4e0d-4859-8d74-9fd3b1da38cb