UPDATE: According to commenter krhodes1 and Facebook commenter Michael Smith, the 228i manual (order code 162A) is still available and there is a bug in the configurator. Which reminds me, you should like The Truth About Cars on Facebook.
Jalopnik is reporting that a number of BMW models — namely the 228i, 328i, and 428i — have lost their manual options for 2016. BMW’s online configurator for the 2016 model year shows the cars as automatic-only options, effectively making the manual transmission a premium option by forcing manual-loving customers into higher trims.
Does this mean the end of the manual transmission as we know it? Probably not. (Yet.)