Regular packages possibly specified as arguments along with --sysupgrade should now be ignored by core update, and core packages should now be skipped in regular update. In this example we can see that ruby is now installed as regular update, and that the filesystem warning is not anymore duplicated:
$ pacman --sync --sysupgrade
:: Starting core system upgrade...
warning: filesystem: local (2016.05-2) is newer than msys (2016.05-1)
+warning: pacman: local (5.0.1.6419.75120af-1) is newer than msys (5.0.1.6403.520736d-1)
there is nothing to do
:: Starting full system upgrade...
-warning: filesystem: local (2016.05-2) is newer than msys (2016.05-1)
there is nothing to do
$ pacman --sync --sysupgrade ruby
warning: ruby-2.3.0-2 is up to date -- reinstalling
:: Starting core system upgrade...
warning: filesystem: local (2016.05-2) is newer than msys (2016.05-1)
-warning: terminate other MSYS2 programs before proceeding
+warning: pacman: local (5.0.1.6419.75120af-1) is newer than msys (5.0.1.6403.520736d-1)
+ there is nothing to do
+:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...
Packages (1) ruby-2.3.0-2
Total Installed Size: 19.80 MiB
Net Upgrade Size: 0.00 MiB
:: Proceed with installation? [Y/n] no
Regular packages possibly specified as arguments along with --sysupgrade should now be ignored by core update, and core packages should now be skipped in regular update. In this example we can see that ruby is now installed as regular update, and that the filesystem warning is not anymore duplicated: