What? It was suggested that the macros should be moved to AppUserHome/Macro http://forum.freecadweb.org/viewtopic.php?f=10&t=13433
Solution: The solution is backwards compatible in the sense that if you have a running configuration, updating should not change anything.
For new installations the macro directory will default to AppUserHome/Macro. However this would break all the installation scripts (probably also ME's plugin manager).