fixed version location for FASTQC and output directory, removed outputDir setting in TRIM

* fixed FASTQC so that version information is properly placed in the
output directory.
* changed the default FASTQC output directory to be “fastqc”.
* in PIPELINE, changed where the FASTQC output on the trimmed data
resides.
* TRIM no longer allows user to set the output directory. This would
break STATS.