Hi!
When designing the ContentHandler, I asked around about whether JS and CSS pages should be parsed as wikitext, so categories etc would work. The gist of the responses I got was "naw, lets get rid of that". So I did (though PST is still applied - Tim asked for that at the Berlin Hackathon).
Sure enough, people are complaining now, see https://bugzilla.wikimedia.org/show_bug.cgi?id=41155. Also note that an older request for disablingt parsing of script pages was closed as WONTFIX: https://bugzilla.wikimedia.org/show_bug.cgi?id=32858.
I'm inclined to (at least optionally) enable the parsing of script pages, but I'd like to get some feedback first.
-- daniel