First time adding custom files, removed example file in custom. The different structure of custom folder from the upstream version is taken care of in oh-my-zsh script
Git will not ignore files in custom directory now
Changes to the way oh-my-zsh sources config scripts. First off, custom folder plugins now go directly into $ZSH/custom directory instead of $ZSH/plugin. I see no reason to have this folder in custom. Secondly, oh-my-zsh will now first look what scripts have been specified in custom. If they happen to have the same name $ZSH/lib, then they are sourced instead (i.e. custom files now properly override oh-my-zsh settings). I decided to do this so that I can have direct control over what oh-my-zsh does to my shell without modifying the upstream script files.