organization of report directory

[taylorreiter]

Could be nice if it was organized like: report/index.html, report/index.ipynb, report/stage2.html, report/stage2.ipynb report/alignments/*.align.html, report/alignments/*.align.ipynb, report/taxonomy/*.fig.html, report/taxonomy/*.fig.ipynb

That way, with large collections of genomes, the summary reports will be immediately available, and the alignment and taxonomy folders could signpost as to what they contain.

Haven't looked at the code to see how annoying this would be to change but my intuition is it would be only mildly annoying to switch over 😄