Have you considered splitting your OS X configuration away from your home-brew installation and other stuff so it's purely an OSX configuration repo?

I have done something similar here: https://github.com/dstroot/.osx

However, I'd rather combine efforts and maybe adopt yours. Thoughts?

The command source installer references a file that doesn't exist. Probably should be source install

Since early betas of OSX El Cap TotalTerminal hasn't launched correctly. After a lot of digging around it was eventually discovered that the new Rootless Protection was hindering TotalTerminal from running correctly. As it's no longer under development, and not natively supported in El Cap, it could be time to remove it from the Cask File application list.
Have you considered replacing it with iTerm2? It doesn't have the great visor functionality that TotalTerminal offered, but it comes close with the hotkey hiding feature. Another option would be to investigate including the disabling of Rootless Protection in Starter.
Thoughts?

Thanks for this project. This is a useful collection to setup my mac. There is one option I added to my script apps/finder.sh.

# Keep folders on top when sorting by name
defaults write com.apple.finder _FXSortFoldersFirst -bool true

regards,
David

line 13: "Srtart"
line 32: "-stirng"
line 80; "-boot"

.. also. This doesn't seem to work anymore:
defaults write com.apple.Safari ProxiesInBookmarksBar '()'

I have a (seemingly ignorant) question. How does this setup compare to OS X's Migration Assistant assuming you are perfectly happy with your current machine setup? Is there a particular reason you prefer having a scripted setup?