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'



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