When dealing with file or path variables, one has to recognize the difference between working with urls and files on disk. For example:
The include() statements are used to include other files (on disk) into the currently running Pm Wiki script. Thus they require paths on the server's filesystem.
The $ScriptUrl and $PubDirUrl variables are used to tell a browser, connecting via the webserver, how to execute the pmwiki script ($ScriptUrl) and the base url for getting files from Pm Wiki's pub/ directory ($PubDirUrl).
is the url that you want people's browsers to use when accessing Pm Wiki, either as a field or farm. It's used whenever Pm Wiki needs to generate a link to another Pm Wiki page or action. Pm Wiki is usually fairly good about "guessing" the correct value for $ScriptUrl on its own, but sometimes an admin needs to set it explicitly because of url manipulations by the webserver (e.g., Cookbook:CleanUrls, mod_rewrite, bizarre PHP configurations, etc.).
is the url that refers to the pub directory. That directory contains all the files and subdirectories that must be directly accessible from a browser (e.g. CSS and HTML files). Most prominent here is the skins subdirectory.
The directory on the server where the farm is located (i.e., the directory containing the farm's copy of pmwiki.php and the scripts/ directory). This directory is automatically determined by pmwiki.php when it runs, and can be used to distinguish the farm's cookbook/ and pub/ subdirectories from a field's subdirectories.
Set by scripts/skins.php to be the base url of the current skin's directory (i.e., within a 'pub/skins/' directory). This variable is typically used inside of a skin .tmpl file to provide access to .css files and graphic images associated with the skin.
The directory where uploads are to be stored. Defaults to uploads/ in the pmwiki directory, but can be set to any location on the server. This directory must be writable by the webserver process if uploading is to occur.
LinkVariables - variables that control the display of links in pages