Added script to automate handling of large number of input files for joi...

...n_paired_ends.py

This is to address cases of when individuals have a lot of already demultiplexed files (standard output on Illumina), and will create/run commands to run join_paired_ends.py on multiple files in a directory that are paired up in some way (e.g. forward reads have "_R1_" and reverse reads have "_R2_" in their names but otherwise have matching names. Also searching a directory of folders is supported (one level down) for paired up fastq files.