Random fixes

* The directories file should be ignored from git (this is machine local).
* Fixed some of the environment settings ($PATH begins with the user's bin dir
* `ll` uses the `ls++` with owners).
* Fixed the setup script (sudmodule is not a real word).
* The XDG environment variables are set in the zshrc
Setup needs to make the directories file
Changed how the `..` alias works in shell

Removed a bunch of unused aliases, added a script to handle expansion of a lot of
parent locations (taken from a SO thread)