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With Quicksilver (and other launchers of that type) you can configure it to index applications from places other than /Applications. I often like to launch things from /System/Library/CoreServices directly, like Software Update. Is there any way to configure Spotlight -- perhaps through the command-line -- to index the applications in that directory?

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Spotlight does index system files by default, but they're just not displayed in the GUI:

$ mdfind -name "software update" | head -n 2
/Library/Preferences/com.apple.SoftwareUpdate.plist
/System/Library/CoreServices/Software Update.app

There's an option to include system files in Finder's Spotlight windows:

I don't know any way to make that the default though. (Or to include them at all in the Spotlight menu.)

One workaround would be to make aliases of everything in CoreServices to somewhere like /Applications/CoreServices/.

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There is a SmartFolder plist file inside the Finder.app that stores the default search. Unfortunately, it does not seem to behave the same as a regular SmartFolder. I've tried editing it several times with very limited effect – username Oct 16 '11 at 19:20
    
@username I've tried that too (on both 10.6 and 10.7). I had modified default_smart.plist to search by filename by default on 10.6, but even that stopped working in Lion. – user495470 Oct 16 '11 at 19:33

I haven't found a way with Spotlight but Alfred lets you add other search folders you can add CoreServices here and that works

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