I think the modification of the fileroot application scoped variable is deprecated in favour of configuring the CDN location that you are working with (note: the local file system corresponds to the "local" CDN type, e.g.
cdn="local" in the code below).
_serverSpecificVarsAfterInit.cfm you can add;
You can change the settings for any of the built-in CDN locations, and you can even define your own locations if the need arises
For some more info see https://farcry.jira.com/wiki/display/FCDEV60/Working+With+CDNs