Hey @nybill, you don't have fancy URLs enabled :O So everything has to be prefixed with "/index.php/". That causes problems with discovery. Of course it should be handled better, but I think that might be one source of problems.
I don't think you should fix this by enabling fancy URLs directly (that could cause other issues with at least !sn, probably !gnusocial too, because of change of URIs). However, maybe you could add a rewrite for any request starting with /.well-known ? I.e. let #nginx rewrite (internally, not redirect) /.well-known/(.*) to /index.php/.well-known/$1
cc: @knuthollund