Simplify usage by removing option data from output file name

Enhancements

1. Greatly simplify usage by deleting most intermediate files automatically rather than relying on the user to do this
2. Make miRNA target prediction algorithm an option, rather than have the user specify this in the output file name
3. Further simplification of the final output target file name ("target_predictions.txt")
4. Allows the user to use both fastq.gz and fq.gz file extensions for RNA-Seq data
5. Enable processing when no RNA-Seq data, and hence no expression filtering is applied
6. Add a header to miRanda output

Bug-fixes

1. Enable use of TPM thresholds when not reannotating 3'UTRs
2. Allows transcript ID with version numbers in the double digits
3. Fix a big with the automated TargetScan test
4. Fix bugs associated with empty files, if for example, no 3'UTRs are extended