Join paired ends updates

Moved function `write_synced_barcodes_fastq` and its test code to `format.py` and `test_format.py` respectively as per [#1243](https://github.com/biocore/qiime/issues/1243).

Also:

* Updated to `skbio.io` code.
* removed `test_join_paired_ends.py` as all relevant test code is now in `test_format.py`
Could you replace that link with this one:
http://scikit-bio.org/docs/latest/generated/skbio.io.fastq.html#format-specification