If you want to tie samples to observation maps and demultiplexed sequences, why couple these links so tightly with the observation counts data? What about having ```samples/external_links```, similar to ```samples/ids```? You can still take slices of these arrays if you only want to retrieve certain samples.

Also note that the on-disk size of a BIOM table is not a primary concern. IMO the primary concerns are 1) be able to parse the files and 2) be able to perform table operations efficiently.

I don't know what the revised goals are (I only learned what QiiTa was a week ago), so it may make sense to take your approach. However, I want to be sure that whatever design we decide on doesn't bite us in the ass performance-wise and stays reasonably simple to enable adoption by other developers. If we are aiming to keep interacting with BIOM tables as we currently are, then the design we came up with during the code sprint is the better option.