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A major advantage of spotlight is, if I happen to be logged in as root (hardly ever necessary) I can still use it.
That is not the case with beagle.
Wow, more than one question poped up.
1. you're logged in as root? what purpose for?
2. don't you know that limitation you talk about is daemons not indexing. daemon has to be run as unprivileged, GUI can be run as any user. and yes, search does work.
3. why would be using search as root be MAJOR advantage if you say it is hardly ever necessary?
4. are you lacking good excuses why would spotlight be better than beagle? Face it it is not. If one disables beagle, system provided searching trough files still works. This is not case with spotlight. Disable it, Command-F, type "pdf" and see what it finds, zero.
"3. why would be using search as root be MAJOR advantage if you say it is hardly ever necessary? "
It is hardly ever necessary in Mac OS X, but not in Linux, which can make your life more difficult if you want to perform administrative tasks and you log in as user.