Starting from the cmdline I get the following output - which I guess is correct since none of the listed PlugIns are in that path :) But they weren't in the path before the update either.
I had no lock with the linked VM either - same result as you. ./pharo-ui Pharo.image 2016-09-22 09:22:05.231 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LocalePlugin' 2016-09-22 09:22:05.232 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.232 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.233 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.434 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/UUIDPlugin' 2016-09-22 09:22:05.434 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.435 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.435 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.435 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:05.436 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.436 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.437 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.437 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:05.446 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.447 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.448 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:05.449 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:05.759 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/SqueakFFIPrims' 2016-09-22 09:22:05.759 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/SqueakFFIPrims' 2016-09-22 09:22:05.760 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:05.760 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:09.517 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:12.541 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:12.542 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/InternetConfigPlugin' 2016-09-22 09:22:12.582 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FT2Plugin' 2016-09-22 09:22:12.585 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/MiscPrimitivePlugin' 2016-09-22 09:22:12.589 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/BitBltPlugin' 2016-09-22 09:22:12.589 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/BitBltPlugin' 2016-09-22 09:22:12.609 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/LargeIntegers' 2016-09-22 09:22:12.766 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/FilePlugin' 2016-09-22 09:22:12.821 Pharo[48644:843238] *** -[NSPathStore2 stringByAppendingPathExtension:]: cannot append extension 'bundle/Contents/MacOS/' to path '/opt/pharo5/sep2016dev/pharo-vm/Pharo.app/Contents/MacOS/Plugins/SocketPlugin' -- View this message in context: http://forum.world.st/Pharo-not-running-with-macOS-Sierra-tp4916468p4916540.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.