I've not found I had to do anything to make it correctly indent code when I've been writing Perl, perhaps that's the default for perl-mode? I only find it gets it wrong if I have a regexp containing some sort of unmatched quote or opening bracket, in which case I end up having to append a comment closing it again or it refuses to line up properly :)
Oh, it should certainly correctly indent by default. indent-tabs-mode determines whether it will insert only spaces or whether it will use tab characters (i.e. ASCII 0x09) to replace runs of spaces - which makes the file smaller but also makes the layout ambiguous (and I find can make navigation trickier as the cursor likes to go to one end of the tab or the other rather than in the middle).
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