Hi,
Yes we changed "protocol" to "center". This is just a change in this attribute name (it doesn't change anything in files organization). It was already effective in version 4.4 about 2 years ago. We changed this because users (especially the CATI team) reported that they were not using "protocol" which did not have a clear meaning, and they would need a "center" attribute instead for multicentric studies. So we did.
Changing back is a bit too late for 4.5 and would not be OK for everyone...
so we are interested in a hierarchy center->protocol->subject
This is actually more complex because it would introduce an additional directory level, so all data would need moving (for now we use the data at the same location, just interpreting an attribute differently). Moving data requires a migration script, and is also something that users are afraid of, because there is always a risk of problem during the move and possible data loss, and it makes databases incompatible with earlier versions, so we do that only when absolutely necessary. Moreover users already complain of "too deep directories organization" which makes things painful to explore manually, so we're not sure we want to do that...
Providing an additional organization that you would use and others would not, is completely possible, but it would need afterwards to maintain changes (new data types) in both, so I don't really want to do that myself in the official version also... (however you can always do it for your lab, of course)
All this may be discussed further with the other maintainers and users, of course, but this will definitely not be done before 4.5.
Denis