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`
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