I have been at it and so far the only one that doesn't work is Packal Updater. when i type packal, I get this notification https://goo.gl/wMhb1G and I see https://goo.gl/8dHuQ5 when I click open Graphical application i get https://goo.gl/5NSiEG
and in the debug tab, this is what i see
[2017-08-29 12:34:55][STDERR: input.scriptfilter] mv: rename alfred-bundler-aries/includes to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/includes: Directory not empty
mv: rename alfred-bundler-aries/meta to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/meta: Directory not empty
mv: rename alfred-bundler-aries/wrappers to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/wrappers: Directory not empty
[2017-08-29 12:34:58][ERROR: action.script] mv: rename alfred-bundler-aries/includes to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/includes: Directory not empty
mv: rename alfred-bundler-aries/meta to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/meta: Directory not empty
mv: rename alfred-bundler-aries/wrappers to /Users/eibrahim/Library/Application Support/Alfred 2/Workflow Data/alfred.bundler-aries/wrappers: Directory not empty