IO directory names

[trvrb]

@jameshadfield and @barneypotter24 ---

I'd like to aim for as much consistency as possible between modules. Currently we have:

• sacra/input/
• sacra/output
• flora/downloaded_data/
• augur/builds/zika/prepared/
• augur/builds/zika/processed/
• augur/builds/zika/auspice/
• auspice/data

I think it makes sense to have augur behave differently, but my preference would be to replace the above with:

• sacra/data/
• flora/data/
• augur/builds/zika/prepared/
• augur/builds/zika/processed/
• augur/builds/zika/auspice/
• auspice/data/

It was always easier for me to think about one directory of data files, where both GenomeFastaResults.fasta is dropped into and zika.fasta is parsed into.